Starting phenix.real_space_refine
on Wed Sep 17 07:46:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fhb_50444/09_2025/9fhb_50444.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fhb_50444/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fhb_50444/09_2025/9fhb_50444.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fhb_50444/09_2025/9fhb_50444.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fhb_50444/09_2025/9fhb_50444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fhb_50444/09_2025/9fhb_50444.map"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.050 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.24
  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: 0.55
  Conformation dependent library (CDL) restraints added in 345.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.24
  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: 0.94

  Time building geometry restraints manager: 0.73 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:             2.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.380
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
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 : 16.68
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.021   0.002   ARG D 198 
 TYR   0.092   0.003   TYR B  35 
 PHE   0.016   0.002   PHE D 438 
 TRP   0.039   0.003   TRP D 455 
 HIS   0.009   0.001   HIS A 122 

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

*********************** 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  : 0.175 
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: 0.7458 (tp30)
REVERT: B   94 ASP cc_start: 0.6962 (t70) cc_final: 0.6365 (m-30)
REVERT: B  122 PHE cc_start: 0.8255 (t80) cc_final: 0.7999 (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: 0.6806 (m-30)
REVERT: D  161 LEU cc_start: 0.8743 (mt) cc_final: 0.8331 (mt)
REVERT: D  436 TRP cc_start: 0.8404 (m-90) cc_final: 0.8137 (m-10)
  outliers start: 23
  outliers final: 16
  residues processed: 146
  average time/residue: 0.0645
  time to fit residues: 13.1648
Evaluate side-chains
  128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  97 HIS
B 117 HIS
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 = 0.3789 r_free = 0.3789 target = 0.135355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114678 restraints weight = 14430.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.117980 restraints weight = 8298.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.120171 restraints weight = 5635.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.121585 restraints weight = 4284.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.122469 restraints weight = 3533.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.156   6943  Z= 0.202
  Angle     :  0.727   8.393   9458  Z= 0.368
  Chirality :  0.047   0.158   1023
  Planarity :  0.004   0.040   1200
  Dihedral  : 10.601 112.245   1013
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.52 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 17.23 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.28), residues: 852
  helix:  1.94 (0.31), residues: 284
  sheet: -0.26 (0.46), residues: 113
  loop : -0.24 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  40 
 TYR   0.024   0.002   TYR B  35 
 PHE   0.010   0.002   PHE C 359 
 TRP   0.017   0.002   TRP D 455 
 HIS   0.005   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 6922)
  covalent geometry    : angle       0.70760 ( 9419)
  SS BOND              : bond        0.00401 (   15)
  SS BOND              : angle       1.24663 (   30)
  hydrogen bonds       : bond        0.04143 (  305)
  hydrogen bonds       : angle       5.65398 (  879)
  Misc. bond           : bond        0.11249 (    3)
  link_NAG-ASN         : bond        0.00546 (    3)
  link_NAG-ASN         : angle       5.05036 (    9)

*********************** 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
  142 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 SER cc_start: 0.9028 (m) cc_final: 0.8491 (p)
REVERT: B   35 TYR cc_start: 0.8308 (m-10) cc_final: 0.7478 (m-10)
REVERT: B   57 ASN cc_start: 0.7647 (t0) cc_final: 0.7412 (t0)
REVERT: C  242 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6701 (m-80)
REVERT: C  243 SER cc_start: 0.8150 (p) cc_final: 0.7922 (p)
REVERT: C  354 ASP cc_start: 0.7710 (m-30) cc_final: 0.7437 (m-30)
REVERT: D  360 ASP cc_start: 0.8572 (m-30) cc_final: 0.8042 (m-30)
REVERT: D  396 LYS cc_start: 0.8464 (pttt) cc_final: 0.8075 (pttt)
REVERT: D  436 TRP cc_start: 0.8665 (m-90) cc_final: 0.8394 (m-10)
  outliers start: 32
  outliers final: 23
  residues processed: 132
  average time/residue: 0.0668
  time to fit residues: 12.4921
Evaluate side-chains
  123 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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 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  182 HIS
Chi-restraints excluded: chain C residue  222 THR
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  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  388 VAL
Chi-restraints excluded: chain C residue  390 VAL
Chi-restraints excluded: chain D residue  199 GLN
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
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 26 optimal weight:    0.1980
   chunk 62 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
C 203 ASN
C 208 HIS
** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 464 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.133502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.113201 restraints weight = 14329.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.116390 restraints weight = 8263.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.118519 restraints weight = 5660.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.119944 restraints weight = 4335.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.120926 restraints weight = 3576.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.119   6943  Z= 0.168
  Angle     :  0.652   8.401   9458  Z= 0.330
  Chirality :  0.044   0.153   1023
  Planarity :  0.004   0.046   1200
  Dihedral  : 10.019 109.607    999
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.29 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 17.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.28), residues: 852
  helix:  1.98 (0.32), residues: 286
  sheet: -0.29 (0.53), residues: 74
  loop : -0.12 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  40 
 TYR   0.015   0.002   TYR B  35 
 PHE   0.013   0.002   PHE A 117 
 TRP   0.011   0.001   TRP B  37 
 HIS   0.004   0.001   HIS D 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 6922)
  covalent geometry    : angle       0.63836 ( 9419)
  SS BOND              : bond        0.00364 (   15)
  SS BOND              : angle       1.15640 (   30)
  hydrogen bonds       : bond        0.03663 (  305)
  hydrogen bonds       : angle       5.19551 (  879)
  Misc. bond           : bond        0.08957 (    3)
  link_NAG-ASN         : bond        0.00540 (    3)
  link_NAG-ASN         : angle       3.90730 (    9)

*********************** 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
  137 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8683 (p) cc_final: 0.8365 (p)
REVERT: B   35 TYR cc_start: 0.8510 (m-80) cc_final: 0.7680 (m-10)
REVERT: B   80 ASN cc_start: 0.6826 (t0) cc_final: 0.6460 (t0)
REVERT: C  242 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6714 (m-80)
REVERT: C  354 ASP cc_start: 0.8129 (m-30) cc_final: 0.7602 (m-30)
REVERT: D  360 ASP cc_start: 0.8595 (m-30) cc_final: 0.8277 (m-30)
REVERT: D  396 LYS cc_start: 0.8420 (pttt) cc_final: 0.8131 (pttt)
REVERT: D  436 TRP cc_start: 0.8670 (m-90) cc_final: 0.8421 (m-10)
  outliers start: 31
  outliers final: 24
  residues processed: 127
  average time/residue: 0.0707
  time to fit residues: 12.3832
Evaluate side-chains
  122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
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 B residue    4 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  137 VAL
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  383 VAL
Chi-restraints excluded: chain C residue  388 VAL
Chi-restraints excluded: chain C residue  390 VAL
Chi-restraints excluded: chain D residue  199 GLN
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8984

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.134242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.113786 restraints weight = 14566.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117042 restraints weight = 8533.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.119166 restraints weight = 5873.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.120552 restraints weight = 4516.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.121567 restraints weight = 3753.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   6943  Z= 0.138
  Angle     :  0.609   7.722   9458  Z= 0.306
  Chirality :  0.043   0.165   1023
  Planarity :  0.004   0.048   1200
  Dihedral  :  9.703 106.505    995
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.52 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 19.21 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.29), residues: 852
  helix:  2.03 (0.32), residues: 286
  sheet: -0.35 (0.54), residues: 70
  loop :  0.09 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  40 
 TYR   0.012   0.002   TYR B  35 
 PHE   0.011   0.001   PHE C 359 
 TRP   0.009   0.001   TRP B  37 
 HIS   0.003   0.001   HIS D 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6922)
  covalent geometry    : angle       0.60110 ( 9419)
  SS BOND              : bond        0.00222 (   15)
  SS BOND              : angle       0.85307 (   30)
  hydrogen bonds       : bond        0.03209 (  305)
  hydrogen bonds       : angle       4.90761 (  879)
  Misc. bond           : bond        0.07260 (    3)
  link_NAG-ASN         : bond        0.00443 (    3)
  link_NAG-ASN         : angle       3.11776 (    9)

*********************** 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
  144 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8733 (p) cc_final: 0.8432 (p)
REVERT: B   35 TYR cc_start: 0.8474 (m-80) cc_final: 0.7963 (m-10)
REVERT: B   80 ASN cc_start: 0.6909 (t0) cc_final: 0.6532 (t0)
REVERT: C  242 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6707 (m-80)
REVERT: C  354 ASP cc_start: 0.8062 (m-30) cc_final: 0.7501 (m-30)
REVERT: D  396 LYS cc_start: 0.8426 (pttt) cc_final: 0.8170 (pttt)
REVERT: D  436 TRP cc_start: 0.8644 (m-10) cc_final: 0.8418 (m-10)
  outliers start: 35
  outliers final: 20
  residues processed: 129
  average time/residue: 0.0609
  time to fit residues: 11.3909
Evaluate side-chains
  123 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain C residue  162 ILE
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  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 D residue  157 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:   30.0000
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 103 HIS
C 195 GLN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.133076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112821 restraints weight = 14751.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.116064 restraints weight = 8538.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.118128 restraints weight = 5858.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.119595 restraints weight = 4512.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.120545 restraints weight = 3720.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   6943  Z= 0.146
  Angle     :  0.623   8.172   9458  Z= 0.312
  Chirality :  0.043   0.155   1023
  Planarity :  0.004   0.050   1200
  Dihedral  :  9.512 104.077    991
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.29 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 19.07 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.30), residues: 852
  helix:  2.03 (0.32), residues: 291
  sheet: -0.72 (0.54), residues: 73
  loop :  0.12 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  40 
 TYR   0.011   0.002   TYR C 352 
 PHE   0.012   0.002   PHE A 117 
 TRP   0.009   0.001   TRP D 457 
 HIS   0.003   0.001   HIS D 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6922)
  covalent geometry    : angle       0.61228 ( 9419)
  SS BOND              : bond        0.00351 (   15)
  SS BOND              : angle       1.46951 (   30)
  hydrogen bonds       : bond        0.03177 (  305)
  hydrogen bonds       : angle       4.88255 (  879)
  Misc. bond           : bond        0.07267 (    3)
  link_NAG-ASN         : bond        0.00382 (    3)
  link_NAG-ASN         : angle       2.80772 (    9)

*********************** 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
  148 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 106
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8766 (p) cc_final: 0.8551 (p)
REVERT: B   26 GLU cc_start: 0.7812 (tp30) cc_final: 0.7582 (tp30)
REVERT: B   35 TYR cc_start: 0.8508 (m-80) cc_final: 0.7996 (m-10)
REVERT: B   80 ASN cc_start: 0.6933 (t0) cc_final: 0.6542 (t0)
REVERT: B   92 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8228 (m90)
REVERT: B   94 ASP cc_start: 0.7347 (t70) cc_final: 0.7034 (t0)
REVERT: B  121 GLU cc_start: 0.8336 (tp30) cc_final: 0.8122 (tp30)
REVERT: C  242 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6741 (m-80)
REVERT: C  354 ASP cc_start: 0.8178 (m-30) cc_final: 0.7570 (m-30)
REVERT: D  328 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8160 (mm)
REVERT: D  396 LYS cc_start: 0.8460 (pttt) cc_final: 0.8118 (pttm)
REVERT: D  436 TRP cc_start: 0.8656 (m-10) cc_final: 0.8435 (m-10)
  outliers start: 42
  outliers final: 31
  residues processed: 134
  average time/residue: 0.0662
  time to fit residues: 12.6945
Evaluate side-chains
  133 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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 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   99 ASP
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  163 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  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  361 VAL
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  289 THR
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 12 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0010
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 112 HIS
C 208 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.131463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111234 restraints weight = 14654.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114440 restraints weight = 8558.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.116540 restraints weight = 5879.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.117938 restraints weight = 4521.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.118830 restraints weight = 3746.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   6943  Z= 0.162
  Angle     :  0.630   7.940   9458  Z= 0.315
  Chirality :  0.044   0.198   1023
  Planarity :  0.004   0.045   1200
  Dihedral  :  9.612 103.156    991
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.99 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 19.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.30), residues: 852
  helix:  1.82 (0.32), residues: 298
  sheet: -0.87 (0.51), residues: 87
  loop :  0.02 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  40 
 TYR   0.013   0.002   TYR C 224 
 PHE   0.013   0.002   PHE C 173 
 TRP   0.010   0.001   TRP B  37 
 HIS   0.004   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6922)
  covalent geometry    : angle       0.62057 ( 9419)
  SS BOND              : bond        0.00297 (   15)
  SS BOND              : angle       1.44268 (   30)
  hydrogen bonds       : bond        0.03285 (  305)
  hydrogen bonds       : angle       4.91994 (  879)
  Misc. bond           : bond        0.08555 (    3)
  link_NAG-ASN         : bond        0.00364 (    3)
  link_NAG-ASN         : angle       2.71298 (    9)

*********************** 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
  144 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 103
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (p)
REVERT: B   35 TYR cc_start: 0.8543 (m-80) cc_final: 0.8164 (m-10)
REVERT: B   80 ASN cc_start: 0.6917 (t0) cc_final: 0.6539 (t0)
REVERT: B   92 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8133 (m90)
REVERT: B   94 ASP cc_start: 0.7276 (t70) cc_final: 0.7031 (t0)
REVERT: B  121 GLU cc_start: 0.8401 (tp30) cc_final: 0.8183 (tp30)
REVERT: C  151 LYS cc_start: 0.7792 (mttt) cc_final: 0.7466 (ptpt)
REVERT: C  242 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6735 (m-80)
REVERT: C  354 ASP cc_start: 0.8187 (m-30) cc_final: 0.7573 (m-30)
REVERT: D  328 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8229 (mm)
REVERT: D  360 ASP cc_start: 0.8206 (m-30) cc_final: 0.7737 (m-30)
REVERT: D  396 LYS cc_start: 0.8465 (pttt) cc_final: 0.8130 (pttm)
REVERT: D  436 TRP cc_start: 0.8670 (m-10) cc_final: 0.8452 (m-10)
  outliers start: 41
  outliers final: 33
  residues processed: 129
  average time/residue: 0.0621
  time to fit residues: 11.6423
Evaluate side-chains
  135 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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   76 MET
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  137 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   99 ASP
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  163 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  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  361 VAL
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  289 THR
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
Chi-restraints excluded: chain D residue  397 VAL
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 40 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
C 208 HIS
C 331 GLN
** D 199 GLN ** 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 = 0.131843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.111687 restraints weight = 14478.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114953 restraints weight = 8515.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.117038 restraints weight = 5842.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.118465 restraints weight = 4492.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.119438 restraints weight = 3709.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.117   6943  Z= 0.155
  Angle     :  0.627   7.686   9458  Z= 0.315
  Chirality :  0.044   0.169   1023
  Planarity :  0.004   0.045   1200
  Dihedral  :  9.655 103.034    991
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.34 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 19.92 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.30), residues: 852
  helix:  1.79 (0.32), residues: 298
  sheet: -0.64 (0.53), residues: 75
  loop : -0.02 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  40 
 TYR   0.012   0.002   TYR C 224 
 PHE   0.013   0.002   PHE A 117 
 TRP   0.012   0.001   TRP C 398 
 HIS   0.006   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6922)
  covalent geometry    : angle       0.61827 ( 9419)
  SS BOND              : bond        0.00371 (   15)
  SS BOND              : angle       1.34195 (   30)
  hydrogen bonds       : bond        0.03201 (  305)
  hydrogen bonds       : angle       4.89230 (  879)
  Misc. bond           : bond        0.08420 (    3)
  link_NAG-ASN         : bond        0.00336 (    3)
  link_NAG-ASN         : angle       2.57385 (    9)

*********************** 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
  148 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8531 (p)
REVERT: B   35 TYR cc_start: 0.8520 (m-80) cc_final: 0.8178 (m-10)
REVERT: B   57 ASN cc_start: 0.7514 (t0) cc_final: 0.7286 (t0)
REVERT: B   80 ASN cc_start: 0.6841 (t0) cc_final: 0.6514 (t0)
REVERT: B   92 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8126 (m90)
REVERT: B   94 ASP cc_start: 0.7257 (t70) cc_final: 0.7010 (t0)
REVERT: C  151 LYS cc_start: 0.7650 (mttt) cc_final: 0.7433 (ptpt)
REVERT: C  242 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6766 (m-80)
REVERT: D  328 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8140 (mm)
REVERT: D  360 ASP cc_start: 0.8190 (m-30) cc_final: 0.7736 (m-30)
REVERT: D  396 LYS cc_start: 0.8451 (pttt) cc_final: 0.8134 (pttm)
REVERT: D  436 TRP cc_start: 0.8651 (m-10) cc_final: 0.8442 (m-10)
  outliers start: 39
  outliers final: 32
  residues processed: 131
  average time/residue: 0.0695
  time to fit residues: 13.0471
Evaluate side-chains
  134 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 98
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   36 PHE
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  137 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   99 ASP
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  163 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  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  361 VAL
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  289 THR
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
Chi-restraints excluded: chain D residue  397 VAL
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 10 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.132686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.112582 restraints weight = 14683.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.115839 restraints weight = 8567.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.118023 restraints weight = 5890.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.119487 restraints weight = 4487.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.120412 restraints weight = 3682.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   6943  Z= 0.133
  Angle     :  0.616   9.207   9458  Z= 0.307
  Chirality :  0.043   0.171   1023
  Planarity :  0.004   0.046   1200
  Dihedral  :  9.571 102.888    991
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.23 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 21.33 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.30), residues: 852
  helix:  2.07 (0.32), residues: 285
  sheet: -1.05 (0.50), residues: 91
  loop : -0.01 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  40 
 TYR   0.010   0.001   TYR C 224 
 PHE   0.016   0.002   PHE B 118 
 TRP   0.012   0.001   TRP C 398 
 HIS   0.005   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6922)
  covalent geometry    : angle       0.60979 ( 9419)
  SS BOND              : bond        0.00232 (   15)
  SS BOND              : angle       1.00998 (   30)
  hydrogen bonds       : bond        0.03029 (  305)
  hydrogen bonds       : angle       4.80018 (  879)
  Misc. bond           : bond        0.07466 (    3)
  link_NAG-ASN         : bond        0.00327 (    3)
  link_NAG-ASN         : angle       2.48733 (    9)

*********************** 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
  140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 105
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8441 (p)
REVERT: B   57 ASN cc_start: 0.7611 (t0) cc_final: 0.7363 (t0)
REVERT: B   80 ASN cc_start: 0.6736 (t0) cc_final: 0.6350 (t0)
REVERT: B   92 HIS cc_start: 0.8691 (OUTLIER) cc_final: 0.8133 (m90)
REVERT: C  242 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6798 (m-80)
REVERT: D  161 LEU cc_start: 0.8685 (tp) cc_final: 0.8347 (pt)
REVERT: D  289 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8808 (p)
REVERT: D  396 LYS cc_start: 0.8377 (pttt) cc_final: 0.8072 (pttm)
REVERT: D  436 TRP cc_start: 0.8637 (m-10) cc_final: 0.8427 (m-10)
  outliers start: 35
  outliers final: 27
  residues processed: 126
  average time/residue: 0.0746
  time to fit residues: 13.2761
Evaluate side-chains
  128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  137 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   99 ASP
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  163 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  261 ARG
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  361 VAL
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  289 THR
Chi-restraints excluded: chain D residue  302 VAL
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  373 LEU
Chi-restraints excluded: chain D residue  397 VAL
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0050
   chunk 47 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 250 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.133410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.113319 restraints weight = 14474.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.116514 restraints weight = 8406.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118718 restraints weight = 5805.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.120237 restraints weight = 4424.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.121277 restraints weight = 3606.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.098   6943  Z= 0.125
  Angle     :  0.622   8.056   9458  Z= 0.309
  Chirality :  0.043   0.182   1023
  Planarity :  0.004   0.070   1200
  Dihedral  :  9.495 101.878    990
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.34 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 21.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.30), residues: 852
  helix:  2.00 (0.32), residues: 290
  sheet: -1.08 (0.51), residues: 91
  loop : -0.11 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  40 
 TYR   0.010   0.001   TYR C 280 
 PHE   0.014   0.001   PHE B 118 
 TRP   0.013   0.001   TRP C 398 
 HIS   0.005   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6922)
  covalent geometry    : angle       0.61596 ( 9419)
  SS BOND              : bond        0.00273 (   15)
  SS BOND              : angle       0.94614 (   30)
  hydrogen bonds       : bond        0.02915 (  305)
  hydrogen bonds       : angle       4.78094 (  879)
  Misc. bond           : bond        0.07021 (    3)
  link_NAG-ASN         : bond        0.00318 (    3)
  link_NAG-ASN         : angle       2.42273 (    9)

*********************** 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
  134 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8456 (p)
REVERT: B    6 GLU cc_start: 0.8115 (pm20) cc_final: 0.7912 (pm20)
REVERT: B   80 ASN cc_start: 0.6605 (t0) cc_final: 0.6290 (t0)
REVERT: B   92 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8126 (m90)
REVERT: C  242 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6839 (m-80)
REVERT: D  396 LYS cc_start: 0.8322 (pttt) cc_final: 0.8005 (pttm)
  outliers start: 33
  outliers final: 27
  residues processed: 121
  average time/residue: 0.0716
  time to fit residues: 12.3612
Evaluate side-chains
  124 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  137 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 HIS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  117 HIS
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  163 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  261 ARG
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  361 VAL
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  256 VAL
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  302 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
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0980
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 26 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 396 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 = 0.3775 r_free = 0.3775 target = 0.134342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.114235 restraints weight = 14555.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.117544 restraints weight = 8463.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.119712 restraints weight = 5801.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.121206 restraints weight = 4418.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.122179 restraints weight = 3620.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088   6943  Z= 0.119
  Angle     :  0.619   8.259   9458  Z= 0.306
  Chirality :  0.043   0.154   1023
  Planarity :  0.004   0.046   1200
  Dihedral  :  9.308 100.486    990
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.46 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.88 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.30), residues: 852
  helix:  2.10 (0.32), residues: 290
  sheet: -1.02 (0.52), residues: 81
  loop : -0.06 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  40 
 TYR   0.013   0.001   TYR C 280 
 PHE   0.012   0.001   PHE A 117 
 TRP   0.013   0.001   TRP C 398 
 HIS   0.004   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6922)
  covalent geometry    : angle       0.61452 ( 9419)
  SS BOND              : bond        0.00233 (   15)
  SS BOND              : angle       0.87819 (   30)
  hydrogen bonds       : bond        0.02840 (  305)
  hydrogen bonds       : angle       4.71129 (  879)
  Misc. bond           : bond        0.06361 (    3)
  link_NAG-ASN         : bond        0.00317 (    3)
  link_NAG-ASN         : angle       2.34172 (    9)

********************** 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
  133 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8494 (p)
REVERT: B   92 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8202 (m90)
REVERT: C  300 MET cc_start: 0.7307 (mpp) cc_final: 0.7087 (mpp)
REVERT: D  360 ASP cc_start: 0.8119 (m-30) cc_final: 0.7711 (m-30)
REVERT: D  396 LYS cc_start: 0.8248 (pttt) cc_final: 0.7959 (pttm)
  outliers start: 29
  outliers final: 26
  residues processed: 123
  average time/residue: 0.0694
  time to fit residues: 12.0536
Evaluate side-chains
  123 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 HIS
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  117 HIS
Chi-restraints excluded: chain C residue  162 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  222 THR
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  261 ARG
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  361 VAL
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  256 VAL
Chi-restraints excluded: chain D residue  269 VAL
Chi-restraints excluded: chain D residue  302 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
Chi-restraints excluded: chain D residue  471 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.134411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114545 restraints weight = 14579.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.117844 restraints weight = 8420.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.120067 restraints weight = 5743.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.121573 restraints weight = 4343.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.122565 restraints weight = 3537.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.4210

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= 0.120
  Angle     :  0.619   8.094   9458  Z= 0.307
  Chirality :  0.043   0.164   1023
  Planarity :  0.004   0.044   1200
  Dihedral  :  9.121  99.059    988
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.11 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 23.73 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.30), residues: 852
  helix:  2.08 (0.32), residues: 290
  sheet: -1.03 (0.52), residues: 81
  loop : -0.05 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  40 
 TYR   0.011   0.001   TYR C 280 
 PHE   0.017   0.001   PHE B 118 
 TRP   0.013   0.001   TRP C 398 
 HIS   0.004   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6922)
  covalent geometry    : angle       0.61392 ( 9419)
  SS BOND              : bond        0.00227 (   15)
  SS BOND              : angle       0.84628 (   30)
  hydrogen bonds       : bond        0.02928 (  305)
  hydrogen bonds       : angle       4.71197 (  879)
  Misc. bond           : bond        0.06132 (    3)
  link_NAG-ASN         : bond        0.00319 (    3)
  link_NAG-ASN         : angle       2.32159 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1188.06 seconds
wall clock time: 21 minutes 26.06 seconds (1286.06 seconds total)