Starting phenix.real_space_refine
on Sun Apr  5 11:05:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ynr_73228/04_2026/9ynr_73228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ynr_73228/04_2026/9ynr_73228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ynr_73228/04_2026/9ynr_73228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ynr_73228/04_2026/9ynr_73228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ynr_73228/04_2026/9ynr_73228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ynr_73228/04_2026/9ynr_73228.cif"
  }
  resolution = 3.55
  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=  -0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    6164      2.51       5
     N    1595      2.21       5
     O    1883      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9679
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "B"
      Number of atoms: 2116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2116
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 15, 'TRANS': 252}
    Chain: "C"
      Number of atoms: 4053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 4053
          Classifications: {'peptide': 508}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 29, 'TRANS': 478}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1753
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 14, 'TRANS': 214}
    Chain: "E"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1575
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197}
    Chain: "A"
      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: "F"
      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: "G"
      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: "H"
      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: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 2.39, per 1000 atoms: 0.25
  Number of scatterers: 9679
  At special positions: 0
  Unit cell: (127.513, 112.413, 119.963, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1883      8.00
     N    1595      7.00
     C    6164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  15 " - pdb=" SG  CYS C 136 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 155 " - pdb=" SG  CYS D 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 135 " - pdb=" SG  CYS E 194 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG A   1 " - " ASN B 343 "
      " NAG B1301 " - " ASN B 331 "
      " NAG C1301 " - " ASN C 165 "
      " NAG C1302 " - " ASN C  61 "
      " NAG C1303 " - " ASN C 343 "
      " NAG C1304 " - " ASN C 331 "
      " NAG F   1 " - " ASN C 122 "
      " NAG G   1 " - " ASN C 234 "
      " NAG H   1 " - " ASN C 282 "
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 468.2 milliseconds
  

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2270

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 29 sheets defined
      8.8% alpha, 33.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.597A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.146A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 3.545A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
      removed outlier: 3.577A  pdb=" N   ILE B 410 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'C' and resid 294 through 304
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.655A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 386 through 390
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 3.887A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'D' and resid 65 through 68
      removed outlier: 3.524A  pdb=" N   LYS D  68 " --> pdb=" O   VAL D  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 65 through 68'
    Processing helix  chain 'D' and resid 147 through 150
    Processing helix  chain 'D' and resid 171 through 173
      No H-bonds generated for 'chain 'D' and resid 171 through 173'
    Processing helix  chain 'E' and resid 81 through 85
      removed outlier: 3.965A  pdb=" N   GLU E  85 " --> pdb=" O   ALA E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 128
    Processing helix  chain 'E' and resid 182 through 187
    Processing helix  chain 'E' and resid 208 through 213
    Processing sheet with id=AA1, first strand: chain 'B' and resid 324 through 328
      removed outlier: 4.053A  pdb=" N   GLU B 324 " --> pdb=" O   CYS B 538 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG B 328 " --> pdb=" O   ASN B 542 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   PHE B 543 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA3, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.574A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA6, first strand: chain 'B' and resid 565 through 566
      removed outlier: 7.324A  pdb=" N   PHE B 565 " --> pdb=" O   PHE C  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 30
    Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 55
      removed outlier: 3.636A  pdb=" N   VAL C 289 " --> pdb=" O   LEU C 276 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 68
      removed outlier: 5.280A  pdb=" N   HIS C  66 " --> pdb=" O   TYR C 265 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   TYR C 265 " --> pdb=" O   HIS C  66 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 85
      removed outlier: 3.556A  pdb=" N   LEU C 244 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 84 through 85
      removed outlier: 6.805A  pdb=" N   ARG C 237 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   PHE C 106 " --> pdb=" O   ARG C 237 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLN C 239 " --> pdb=" O   TRP C 104 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TRP C 104 " --> pdb=" O   GLN C 239 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU C 241 " --> pdb=" O   ARG C 102 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL C 130 " --> pdb=" O   THR C 167 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLU C 132 " --> pdb=" O   ASN C 165 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASN C 165 " --> pdb=" O   GLU C 132 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   GLN C 134 " --> pdb=" O   ALA C 163 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ALA C 163 " --> pdb=" O   GLN C 134 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 126 through 127
    Processing sheet with id=AB4, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AB5, first strand: chain 'C' and resid 354 through 358
      removed outlier: 4.080A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AB8, first strand: chain 'C' and resid 539 through 543
    Processing sheet with id=AB9, first strand: chain 'C' and resid 565 through 566
      removed outlier: 3.511A  pdb=" N   ALA C 575 " --> pdb=" O   GLY C 566 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 7
      removed outlier: 3.578A  pdb=" N   SER D  83 " --> pdb=" O   ASN D  74 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 60 through 63
      removed outlier: 6.470A  pdb=" N   ARG D 101 " --> pdb=" O   ASP D 116 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLY D 114 " --> pdb=" O   GLU D 103 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 46 through 48
    Processing sheet with id=AC4, first strand: chain 'D' and resid 135 through 139
      removed outlier: 4.147A  pdb=" N   GLY D 154 " --> pdb=" O   LEU D 139 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   TYR D 191 " --> pdb=" O   ASP D 159 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER D 192 " --> pdb=" O   VAL D 184 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 166 through 169
    Processing sheet with id=AC6, first strand: chain 'E' and resid 9 through 12
      removed outlier: 6.229A  pdb=" N   GLN E  39 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   LEU E  48 " --> pdb=" O   GLN E  39 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 9 through 12
    Processing sheet with id=AC8, first strand: chain 'E' and resid 18 through 23
    Processing sheet with id=AC9, first strand: chain 'E' and resid 115 through 119
      removed outlier: 3.761A  pdb=" N   PHE E 119 " --> pdb=" O   VAL E 134 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   VAL E 134 " --> pdb=" O   PHE E 119 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TYR E 173 " --> pdb=" O   ASP E 139 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 115 through 119
      removed outlier: 3.761A  pdb=" N   PHE E 119 " --> pdb=" O   VAL E 134 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   VAL E 134 " --> pdb=" O   PHE E 119 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TYR E 173 " --> pdb=" O   ASP E 139 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 154 through 155

    304 hydrogen bonds defined for protein.
    729 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.67

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3033
        1.34 -     1.46: 2283
        1.46 -     1.58: 4565
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 9920
  Sorted by residual:
  bond pdb=" N   GLN C 115 "
       pdb=" CA  GLN C 115 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.034 1.16e-02 7.43e+03 8.70e+00
  bond pdb=" N   VAL C 130 "
       pdb=" CA  VAL C 130 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.24e-02 6.50e+03 7.61e+00
  bond pdb=" N   PHE C 168 "
       pdb=" CA  PHE C 168 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.18e-02 7.18e+03 7.47e+00
  bond pdb=" N   ASN C 164 "
       pdb=" CA  ASN C 164 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.23e-02 6.61e+03 7.26e+00
  bond pdb=" N   LEU C 117 "
       pdb=" CA  LEU C 117 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.96e+00
  ... (remaining 9915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 13113
        1.70 -     3.40: 352
        3.40 -     5.10: 35
        5.10 -     6.81: 6
        6.81 -     8.51: 3
  Bond angle restraints: 13509
  Sorted by residual:
  angle pdb=" CA  GLU C 132 "
        pdb=" C   GLU C 132 "
        pdb=" O   GLU C 132 "
      ideal   model   delta    sigma   weight residual
     122.64  118.23    4.41 1.25e+00 6.40e-01 1.24e+01
  angle pdb=" CA  CYS C 131 "
        pdb=" C   CYS C 131 "
        pdb=" O   CYS C 131 "
      ideal   model   delta    sigma   weight residual
     121.38  118.03    3.35 1.06e+00 8.90e-01 1.00e+01
  angle pdb=" CA  CYS C 166 "
        pdb=" C   CYS C 166 "
        pdb=" O   CYS C 166 "
      ideal   model   delta    sigma   weight residual
     121.56  118.17    3.39 1.09e+00 8.42e-01 9.69e+00
  angle pdb=" CA  ASN C 165 "
        pdb=" C   ASN C 165 "
        pdb=" O   ASN C 165 "
      ideal   model   delta    sigma   weight residual
     121.84  118.24    3.60 1.16e+00 7.43e-01 9.63e+00
  angle pdb=" C   ILE D 210 "
        pdb=" N   CYS D 211 "
        pdb=" CA  CYS D 211 "
      ideal   model   delta    sigma   weight residual
     120.87  125.05   -4.18 1.42e+00 4.96e-01 8.68e+00
  ... (remaining 13504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 5331
       17.89 -    35.77: 523
       35.77 -    53.66: 142
       53.66 -    71.55: 46
       71.55 -    89.43: 12
  Dihedral angle restraints: 6054
    sinusoidal: 2512
      harmonic: 3542
  Sorted by residual:
  dihedral pdb=" CB  CYS D 155 "
           pdb=" SG  CYS D 155 "
           pdb=" SG  CYS D 211 "
           pdb=" CB  CYS D 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.79  -88.21     1      1.00e+01 1.00e-02 9.30e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.58  -87.42     1      1.00e+01 1.00e-02 9.17e+01
  dihedral pdb=" CB  CYS E 135 "
           pdb=" SG  CYS E 135 "
           pdb=" SG  CYS E 194 "
           pdb=" CB  CYS E 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.90  -66.90     1      1.00e+01 1.00e-02 5.83e+01
  ... (remaining 6051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1111
       0.046 -    0.091: 324
       0.091 -    0.137: 93
       0.137 -    0.183: 5
       0.183 -    0.229: 5
  Chirality restraints: 1538
  Sorted by residual:
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN C 282 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  ILE C 128 "
            pdb=" N   ILE C 128 "
            pdb=" C   ILE C 128 "
            pdb=" CB  ILE C 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" C1  NAG C1301 "
            pdb=" ND2 ASN C 165 "
            pdb=" C2  NAG C1301 "
            pdb=" O5  NAG C1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 1535 not shown)

  Planarity restraints: 1732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 120 "    0.011 2.00e-02 2.50e+03   2.29e-02 5.23e+00
        pdb=" C   VAL C 120 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   VAL C 120 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN C 121 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D  93 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.45e+00
        pdb=" C   ASP D  93 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASP D  93 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR D  94 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C  99 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   ASN C  99 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASN C  99 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE C 100 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1729 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 4057
        2.90 -     3.40: 8468
        3.40 -     3.90: 15646
        3.90 -     4.40: 17450
        4.40 -     4.90: 30056
  Nonbonded interactions: 75677
  Sorted by model distance:
  nonbonded pdb=" O   ASP D  93 "
            pdb=" OD1 ASP D  93 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" O   THR B 430 "
            pdb=" OG1 THR B 430 "
     model   vdw
     2.460 3.040
  nonbonded pdb=" OD1 ASP E 139 "
            pdb=" OE1 GLN E 168 "
     model   vdw
     2.492 3.040
  nonbonded pdb=" O   ASN C  99 "
            pdb=" OD1 ASN C  99 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" N   GLU C 224 "
            pdb=" OE1 GLU C 224 "
     model   vdw
     2.552 3.120
  ... (remaining 75672 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             9.080
  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:          0.250
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.030
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
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   0.046   9948  Z= 0.243
  Angle     :  0.658   8.507  13578  Z= 0.366
  Chirality :  0.047   0.229   1538
  Planarity :  0.005   0.063   1723
  Dihedral  : 15.781  89.434   3739
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 22.86 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.43 (0.23), residues: 1191
  helix: -1.74 (0.53), residues: 94
  sheet: -0.44 (0.26), residues: 376
  loop : -1.11 (0.22), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 357 
 TYR   0.017   0.002   TYR C 279 
 PHE   0.023   0.002   PHE B 377 
 TRP   0.010   0.002   TRP B 436 
 HIS   0.003   0.001   HIS C 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 9920)
  covalent geometry    : angle       0.64932 (13509)
  SS BOND              : bond        0.00435 (   15)
  SS BOND              : angle       1.31651 (   30)
  hydrogen bonds       : bond        0.14162 (  278)
  hydrogen bonds       : angle       7.81136 (  729)
  link_BETA1-4         : bond        0.00346 (    4)
  link_BETA1-4         : angle       1.52725 (   12)
  link_NAG-ASN         : bond        0.00776 (    9)
  link_NAG-ASN         : angle       1.99920 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 210
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  428 ASP cc_start: 0.7731 (p0) cc_final: 0.7401 (p0)
REVERT: B  574 ASP cc_start: 0.7066 (p0) cc_final: 0.6829 (p0)
REVERT: C   69 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6928 (t-90)
REVERT: C  392 PHE cc_start: 0.6666 (m-80) cc_final: 0.6330 (m-10)
REVERT: D  150 THR cc_start: 0.8661 (p) cc_final: 0.8367 (t)
REVERT: D  158 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7721 (ttpp)
REVERT: D  226 VAL cc_start: 0.6586 (t) cc_final: 0.6336 (t)
REVERT: E  133 LEU cc_start: 0.8274 (mp) cc_final: 0.7847 (mt)
  outliers start: 10
  outliers final: 2
  residues processed: 214
  average time/residue: 0.1229
  time to fit residues: 34.9203
Evaluate side-chains
  119 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 116
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  585 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
B 563 GLN
C 121 ASN
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 195 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.102315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.071510 restraints weight = 29094.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.074209 restraints weight = 14318.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.075859 restraints weight = 9589.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.076844 restraints weight = 7563.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.077483 restraints weight = 6528.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   9948  Z= 0.274
  Angle     :  0.705  10.140  13578  Z= 0.355
  Chirality :  0.047   0.215   1538
  Planarity :  0.005   0.039   1723
  Dihedral  :  6.159  53.440   1594
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 22.48 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.44 (0.24), residues: 1191
  helix: -1.89 (0.49), residues: 103
  sheet: -0.54 (0.25), residues: 397
  loop : -1.02 (0.23), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 357 
 TYR   0.032   0.002   TYR D 111 
 PHE   0.016   0.002   PHE D  82 
 TRP   0.011   0.002   TRP D  59 
 HIS   0.004   0.001   HIS D 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 9920)
  covalent geometry    : angle       0.69546 (13509)
  SS BOND              : bond        0.00593 (   15)
  SS BOND              : angle       1.72694 (   30)
  hydrogen bonds       : bond        0.03907 (  278)
  hydrogen bonds       : angle       6.55038 (  729)
  link_BETA1-4         : bond        0.00575 (    4)
  link_BETA1-4         : angle       1.43147 (   12)
  link_NAG-ASN         : bond        0.00511 (    9)
  link_NAG-ASN         : angle       1.84648 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 115
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8559 (ttpp)
REVERT: B  406 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8346 (mm-30)
REVERT: C   69 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6829 (t-90)
REVERT: C  490 PHE cc_start: 0.8371 (t80) cc_final: 0.7538 (t80)
REVERT: D   62 ASP cc_start: 0.8215 (t0) cc_final: 0.8004 (t0)
REVERT: D  101 ARG cc_start: 0.8125 (ttt-90) cc_final: 0.7624 (ttt-90)
REVERT: D  103 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7893 (tp30)
REVERT: D  108 HIS cc_start: 0.8232 (t-90) cc_final: 0.7796 (t-90)
REVERT: D  132 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8220 (ptmm)
REVERT: E  119 PHE cc_start: 0.6801 (m-80) cc_final: 0.6598 (m-80)
  outliers start: 52
  outliers final: 24
  residues processed: 161
  average time/residue: 0.0976
  time to fit residues: 22.4126
Evaluate side-chains
  130 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  378 LYS
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain C residue  211 ASN
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  286 THR
Chi-restraints excluded: chain C residue  294 ASP
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  585 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  132 LYS
Chi-restraints excluded: chain D residue  156 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  166 SER
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 87 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 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 = 0.3861 r_free = 0.3861 target = 0.102949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.072380 restraints weight = 29057.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.075141 restraints weight = 14159.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.076812 restraints weight = 9460.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077860 restraints weight = 7401.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.078499 restraints weight = 6358.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9948  Z= 0.155
  Angle     :  0.619  10.494  13578  Z= 0.309
  Chirality :  0.046   0.279   1538
  Planarity :  0.004   0.037   1723
  Dihedral  :  6.023  53.784   1594
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 22.67 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.33 (0.24), residues: 1191
  helix: -1.68 (0.52), residues: 97
  sheet: -0.53 (0.26), residues: 391
  loop : -0.93 (0.23), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 567 
 TYR   0.018   0.001   TYR D 111 
 PHE   0.028   0.001   PHE C 329 
 TRP   0.012   0.001   TRP D  36 
 HIS   0.002   0.001   HIS E 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9920)
  covalent geometry    : angle       0.61071 (13509)
  SS BOND              : bond        0.00443 (   15)
  SS BOND              : angle       1.47624 (   30)
  hydrogen bonds       : bond        0.03363 (  278)
  hydrogen bonds       : angle       6.30109 (  729)
  link_BETA1-4         : bond        0.00320 (    4)
  link_BETA1-4         : angle       1.36108 (   12)
  link_NAG-ASN         : bond        0.00380 (    9)
  link_NAG-ASN         : angle       1.58935 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 106
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8241 (mm-30)
REVERT: B  574 ASP cc_start: 0.7323 (p0) cc_final: 0.6923 (p0)
REVERT: C   69 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6838 (t-90)
REVERT: C  200 TYR cc_start: 0.7527 (m-80) cc_final: 0.7230 (t80)
REVERT: C  365 TYR cc_start: 0.5865 (m-10) cc_final: 0.5610 (m-10)
REVERT: C  392 PHE cc_start: 0.8100 (m-80) cc_final: 0.7615 (m-80)
REVERT: C  515 PHE cc_start: 0.7911 (m-80) cc_final: 0.7172 (m-80)
REVERT: D   62 ASP cc_start: 0.8191 (t0) cc_final: 0.7959 (t0)
REVERT: D  108 HIS cc_start: 0.8261 (t-90) cc_final: 0.7811 (t-90)
REVERT: D  111 TYR cc_start: 0.8559 (m-80) cc_final: 0.8339 (m-80)
REVERT: E  125 GLU cc_start: 0.8237 (tp30) cc_final: 0.7973 (mm-30)
  outliers start: 42
  outliers final: 24
  residues processed: 141
  average time/residue: 0.1015
  time to fit residues: 20.3872
Evaluate side-chains
  126 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  211 ASN
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  294 ASP
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  156 LEU
Chi-restraints excluded: chain D residue  159 ASP
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C 542 ASN
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 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 = 0.3858 r_free = 0.3858 target = 0.102848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.072330 restraints weight = 29320.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.075095 restraints weight = 14263.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.076725 restraints weight = 9503.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077811 restraints weight = 7477.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.078484 restraints weight = 6403.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9948  Z= 0.148
  Angle     :  0.601  10.212  13578  Z= 0.299
  Chirality :  0.046   0.292   1538
  Planarity :  0.004   0.038   1723
  Dihedral  :  5.839  53.464   1592
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.42 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.19 (0.24), residues: 1191
  helix: -1.46 (0.56), residues: 90
  sheet: -0.33 (0.27), residues: 365
  loop : -0.93 (0.22), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 101 
 TYR   0.013   0.001   TYR D 111 
 PHE   0.036   0.001   PHE C 329 
 TRP   0.011   0.001   TRP D  36 
 HIS   0.002   0.001   HIS E 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9920)
  covalent geometry    : angle       0.59444 (13509)
  SS BOND              : bond        0.00580 (   15)
  SS BOND              : angle       1.27505 (   30)
  hydrogen bonds       : bond        0.03180 (  278)
  hydrogen bonds       : angle       6.08685 (  729)
  link_BETA1-4         : bond        0.00373 (    4)
  link_BETA1-4         : angle       1.28111 (   12)
  link_NAG-ASN         : bond        0.00390 (    9)
  link_NAG-ASN         : angle       1.58772 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7860 (tp30)
REVERT: B  493 GLN cc_start: 0.8265 (tp40) cc_final: 0.8063 (tp40)
REVERT: B  574 ASP cc_start: 0.7352 (p0) cc_final: 0.6934 (p0)
REVERT: C   69 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6901 (t-90)
REVERT: C  200 TYR cc_start: 0.7563 (m-80) cc_final: 0.7182 (t80)
REVERT: C  392 PHE cc_start: 0.8000 (m-80) cc_final: 0.7606 (m-80)
REVERT: C  449 TYR cc_start: 0.8598 (m-10) cc_final: 0.7642 (t80)
REVERT: C  515 PHE cc_start: 0.8063 (m-80) cc_final: 0.7257 (m-80)
REVERT: C  559 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.6024 (m-10)
REVERT: D   62 ASP cc_start: 0.8241 (t0) cc_final: 0.7927 (t0)
REVERT: D  103 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8185 (tp30)
REVERT: D  108 HIS cc_start: 0.8346 (t-90) cc_final: 0.7925 (t-90)
REVERT: D  111 TYR cc_start: 0.8586 (m-80) cc_final: 0.8375 (m-80)
  outliers start: 36
  outliers final: 23
  residues processed: 136
  average time/residue: 0.0950
  time to fit residues: 18.5831
Evaluate side-chains
  124 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  211 ASN
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  294 ASP
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  156 LEU
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 63 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 94 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0770
   chunk 13 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0770
   chunk 84 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 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 = 0.3796 r_free = 0.3796 target = 0.101251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.072370 restraints weight = 28311.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.074989 restraints weight = 17169.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.075452 restraints weight = 10249.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.076378 restraints weight = 9142.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.076467 restraints weight = 8386.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9948  Z= 0.113
  Angle     :  0.588   8.678  13578  Z= 0.292
  Chirality :  0.045   0.318   1538
  Planarity :  0.004   0.040   1723
  Dihedral  :  5.706  53.431   1592
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 24.18 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.08 (0.24), residues: 1191
  helix: -1.40 (0.58), residues: 82
  sheet: -0.28 (0.26), residues: 379
  loop : -0.85 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 457 
 TYR   0.012   0.001   TYR D 191 
 PHE   0.027   0.001   PHE C 429 
 TRP   0.012   0.001   TRP D  36 
 HIS   0.002   0.000   HIS E 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9920)
  covalent geometry    : angle       0.58238 (13509)
  SS BOND              : bond        0.00446 (   15)
  SS BOND              : angle       1.16493 (   30)
  hydrogen bonds       : bond        0.02943 (  278)
  hydrogen bonds       : angle       6.06352 (  729)
  link_BETA1-4         : bond        0.00367 (    4)
  link_BETA1-4         : angle       1.21575 (   12)
  link_NAG-ASN         : bond        0.00346 (    9)
  link_NAG-ASN         : angle       1.48581 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8211 (mm-30)
REVERT: B  574 ASP cc_start: 0.7373 (p0) cc_final: 0.6952 (p0)
REVERT: C   69 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6819 (t-90)
REVERT: C  365 TYR cc_start: 0.6075 (m-80) cc_final: 0.5641 (m-10)
REVERT: C  392 PHE cc_start: 0.7767 (m-80) cc_final: 0.7219 (m-80)
REVERT: C  449 TYR cc_start: 0.8248 (m-10) cc_final: 0.7387 (t80)
REVERT: C  515 PHE cc_start: 0.7975 (m-80) cc_final: 0.7547 (m-80)
REVERT: C  559 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5895 (m-10)
REVERT: D   62 ASP cc_start: 0.8082 (t0) cc_final: 0.7820 (t0)
REVERT: D  108 HIS cc_start: 0.8165 (t-90) cc_final: 0.7775 (t-90)
REVERT: D  159 ASP cc_start: 0.8469 (m-30) cc_final: 0.8064 (t0)
REVERT: E  125 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6285 (mm-30)
REVERT: E  211 GLU cc_start: 0.4057 (mt-10) cc_final: 0.3598 (mp0)
  outliers start: 33
  outliers final: 16
  residues processed: 137
  average time/residue: 0.0941
  time to fit residues: 18.6417
Evaluate side-chains
  117 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue   76 THR
Chi-restraints excluded: chain E residue   97 ILE
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 113 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0010
   chunk 44 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0870
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.9568

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

Flipped N/Q/H residues before XYZ refinement:
C  14 GLN
C 506 GLN
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 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 = 0.3771 r_free = 0.3771 target = 0.099810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.070843 restraints weight = 28565.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.073298 restraints weight = 16259.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.073728 restraints weight = 10142.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.074186 restraints weight = 9838.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.074364 restraints weight = 8845.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9948  Z= 0.162
  Angle     :  0.603   8.115  13578  Z= 0.298
  Chirality :  0.046   0.320   1538
  Planarity :  0.004   0.058   1723
  Dihedral  :  5.737  53.115   1592
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.27 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.10 (0.24), residues: 1191
  helix: -1.51 (0.58), residues: 82
  sheet: -0.36 (0.26), residues: 382
  loop : -0.80 (0.23), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 101 
 TYR   0.013   0.001   TYR E  62 
 PHE   0.021   0.001   PHE C 329 
 TRP   0.011   0.001   TRP D  36 
 HIS   0.002   0.001   HIS E 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9920)
  covalent geometry    : angle       0.59612 (13509)
  SS BOND              : bond        0.00417 (   15)
  SS BOND              : angle       1.27430 (   30)
  hydrogen bonds       : bond        0.03097 (  278)
  hydrogen bonds       : angle       5.98161 (  729)
  link_BETA1-4         : bond        0.00389 (    4)
  link_BETA1-4         : angle       1.22859 (   12)
  link_NAG-ASN         : bond        0.00289 (    9)
  link_NAG-ASN         : angle       1.68584 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  574 ASP cc_start: 0.7454 (p0) cc_final: 0.6953 (p0)
REVERT: C   69 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6932 (t-90)
REVERT: C  392 PHE cc_start: 0.7833 (m-80) cc_final: 0.7616 (m-80)
REVERT: C  449 TYR cc_start: 0.8342 (m-10) cc_final: 0.7437 (t80)
REVERT: C  559 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.6131 (m-10)
REVERT: D   32 ASN cc_start: 0.9138 (t0) cc_final: 0.8622 (t0)
REVERT: D   62 ASP cc_start: 0.8199 (t0) cc_final: 0.7914 (t0)
REVERT: D  108 HIS cc_start: 0.8356 (t-90) cc_final: 0.7941 (t-90)
REVERT: D  159 ASP cc_start: 0.8546 (m-30) cc_final: 0.8100 (t0)
REVERT: E  190 ARG cc_start: 0.7424 (tpp80) cc_final: 0.7124 (mmm160)
REVERT: E  211 GLU cc_start: 0.4098 (mt-10) cc_final: 0.3722 (mp0)
  outliers start: 31
  outliers final: 23
  residues processed: 122
  average time/residue: 0.0939
  time to fit residues: 16.5931
Evaluate side-chains
  115 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  211 ASN
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  156 LEU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   18 ILE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  168 GLN
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 104 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 61 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 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 = 0.3771 r_free = 0.3771 target = 0.099832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.070958 restraints weight = 28375.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.073419 restraints weight = 16146.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.073879 restraints weight = 10106.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.074904 restraints weight = 9810.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.075088 restraints weight = 8111.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9948  Z= 0.149
  Angle     :  0.600  10.277  13578  Z= 0.296
  Chirality :  0.046   0.319   1538
  Planarity :  0.004   0.076   1723
  Dihedral  :  5.721  53.353   1592
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.93 %
    Favored  : 72.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.10 (0.24), residues: 1191
  helix: -1.61 (0.56), residues: 88
  sheet: -0.42 (0.26), residues: 385
  loop : -0.75 (0.23), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 346 
 TYR   0.011   0.001   TYR E  62 
 PHE   0.018   0.001   PHE C 329 
 TRP   0.012   0.001   TRP D  36 
 HIS   0.002   0.001   HIS E 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9920)
  covalent geometry    : angle       0.59301 (13509)
  SS BOND              : bond        0.00440 (   15)
  SS BOND              : angle       1.18622 (   30)
  hydrogen bonds       : bond        0.02989 (  278)
  hydrogen bonds       : angle       5.88629 (  729)
  link_BETA1-4         : bond        0.00435 (    4)
  link_BETA1-4         : angle       1.18554 (   12)
  link_NAG-ASN         : bond        0.00251 (    9)
  link_NAG-ASN         : angle       1.71461 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  574 ASP cc_start: 0.7457 (p0) cc_final: 0.6955 (p0)
REVERT: C   69 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.6914 (t-90)
REVERT: C  220 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7663 (t80)
REVERT: C  392 PHE cc_start: 0.7804 (m-80) cc_final: 0.7598 (m-80)
REVERT: C  449 TYR cc_start: 0.8340 (m-10) cc_final: 0.7420 (t80)
REVERT: C  559 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.6176 (m-10)
REVERT: D   32 ASN cc_start: 0.9097 (t0) cc_final: 0.8844 (t0)
REVERT: D   62 ASP cc_start: 0.8188 (t0) cc_final: 0.7888 (t0)
REVERT: D  108 HIS cc_start: 0.8315 (t-90) cc_final: 0.7870 (t-90)
REVERT: D  159 ASP cc_start: 0.8552 (m-30) cc_final: 0.8114 (t0)
REVERT: E  140 PHE cc_start: 0.8060 (p90) cc_final: 0.7854 (p90)
REVERT: E  190 ARG cc_start: 0.7509 (tpp80) cc_final: 0.7154 (mmm160)
REVERT: E  211 GLU cc_start: 0.4138 (mt-10) cc_final: 0.3790 (mp0)
  outliers start: 31
  outliers final: 20
  residues processed: 125
  average time/residue: 0.1013
  time to fit residues: 18.1083
Evaluate side-chains
  113 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  220 PHE
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 104 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 506 GLN
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 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 = 0.3769 r_free = 0.3769 target = 0.099676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.070798 restraints weight = 28439.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.073931 restraints weight = 16626.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.074357 restraints weight = 9594.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.075384 restraints weight = 8536.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.075464 restraints weight = 7566.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9948  Z= 0.150
  Angle     :  0.598  11.052  13578  Z= 0.295
  Chirality :  0.045   0.319   1538
  Planarity :  0.004   0.042   1723
  Dihedral  :  5.705  53.175   1592
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.55 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.09 (0.24), residues: 1191
  helix: -1.64 (0.56), residues: 89
  sheet: -0.43 (0.26), residues: 390
  loop : -0.72 (0.23), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 355 
 TYR   0.014   0.001   TYR D 209 
 PHE   0.026   0.001   PHE C 329 
 TRP   0.007   0.001   TRP B 436 
 HIS   0.002   0.000   HIS E 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9920)
  covalent geometry    : angle       0.59155 (13509)
  SS BOND              : bond        0.00471 (   15)
  SS BOND              : angle       1.21817 (   30)
  hydrogen bonds       : bond        0.02983 (  278)
  hydrogen bonds       : angle       5.87270 (  729)
  link_BETA1-4         : bond        0.00350 (    4)
  link_BETA1-4         : angle       1.17816 (   12)
  link_NAG-ASN         : bond        0.00253 (    9)
  link_NAG-ASN         : angle       1.62658 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  574 ASP cc_start: 0.7480 (p0) cc_final: 0.6997 (p0)
REVERT: C   69 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6859 (t-90)
REVERT: C  220 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7593 (t80)
REVERT: C  449 TYR cc_start: 0.8327 (m-10) cc_final: 0.7434 (t80)
REVERT: C  559 PHE cc_start: 0.6503 (OUTLIER) cc_final: 0.6200 (m-10)
REVERT: D   32 ASN cc_start: 0.9038 (t0) cc_final: 0.8707 (t0)
REVERT: D   40 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8881 (ptt180)
REVERT: D   62 ASP cc_start: 0.8140 (t0) cc_final: 0.7844 (t0)
REVERT: D  108 HIS cc_start: 0.8221 (t-90) cc_final: 0.7958 (t-90)
REVERT: D  159 ASP cc_start: 0.8466 (m-30) cc_final: 0.8058 (t0)
REVERT: E   33 ASN cc_start: 0.9174 (p0) cc_final: 0.8686 (p0)
REVERT: E  190 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7141 (mmm160)
REVERT: E  211 GLU cc_start: 0.4122 (mt-10) cc_final: 0.3850 (mp0)
  outliers start: 31
  outliers final: 22
  residues processed: 121
  average time/residue: 0.0997
  time to fit residues: 17.0903
Evaluate side-chains
  113 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  220 PHE
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  156 LEU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   18 ILE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0570
   chunk 0 optimal weight:    2.9990
   chunk 105 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 101 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.100140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.071402 restraints weight = 28366.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.074231 restraints weight = 15745.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.074452 restraints weight = 9505.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.076035 restraints weight = 9517.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.076089 restraints weight = 7632.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9948  Z= 0.129
  Angle     :  0.610  14.670  13578  Z= 0.297
  Chirality :  0.045   0.299   1538
  Planarity :  0.004   0.042   1723
  Dihedral  :  5.663  53.214   1592
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 24.93 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -1.02 (0.24), residues: 1191
  helix: -1.52 (0.57), residues: 86
  sheet: -0.36 (0.26), residues: 385
  loop : -0.70 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 355 
 TYR   0.012   0.001   TYR D 209 
 PHE   0.022   0.001   PHE C 329 
 TRP   0.011   0.001   TRP D  36 
 HIS   0.002   0.000   HIS E 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9920)
  covalent geometry    : angle       0.60398 (13509)
  SS BOND              : bond        0.00479 (   15)
  SS BOND              : angle       1.13704 (   30)
  hydrogen bonds       : bond        0.02903 (  278)
  hydrogen bonds       : angle       5.84639 (  729)
  link_BETA1-4         : bond        0.00379 (    4)
  link_BETA1-4         : angle       1.13874 (   12)
  link_NAG-ASN         : bond        0.00296 (    9)
  link_NAG-ASN         : angle       1.66829 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  574 ASP cc_start: 0.7321 (p0) cc_final: 0.6875 (p0)
REVERT: C   69 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6864 (t-90)
REVERT: C  220 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: C  449 TYR cc_start: 0.8405 (m-10) cc_final: 0.7496 (t80)
REVERT: C  559 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.6259 (m-10)
REVERT: D   32 ASN cc_start: 0.9100 (t0) cc_final: 0.8768 (t0)
REVERT: D   62 ASP cc_start: 0.8241 (t0) cc_final: 0.7904 (t0)
REVERT: D  108 HIS cc_start: 0.8310 (t-90) cc_final: 0.8004 (t-90)
REVERT: D  159 ASP cc_start: 0.8536 (m-30) cc_final: 0.8065 (t0)
REVERT: E   33 ASN cc_start: 0.9087 (p0) cc_final: 0.8197 (p0)
REVERT: E  190 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7242 (mmm160)
  outliers start: 28
  outliers final: 19
  residues processed: 123
  average time/residue: 0.1013
  time to fit residues: 17.6522
Evaluate side-chains
  114 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  220 PHE
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  156 LEU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   18 ILE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 55 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 185 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.100100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.071730 restraints weight = 28184.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.074311 restraints weight = 17039.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.074923 restraints weight = 10126.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.076492 restraints weight = 8898.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.076602 restraints weight = 7525.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   9948  Z= 0.133
  Angle     :  0.609  11.251  13578  Z= 0.298
  Chirality :  0.046   0.315   1538
  Planarity :  0.004   0.042   1723
  Dihedral  :  5.616  53.065   1592
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 25.21 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -0.98 (0.24), residues: 1191
  helix: -1.56 (0.57), residues: 86
  sheet: -0.30 (0.26), residues: 383
  loop : -0.68 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 355 
 TYR   0.015   0.001   TYR D 209 
 PHE   0.020   0.001   PHE C 329 
 TRP   0.013   0.001   TRP D  36 
 HIS   0.006   0.001   HIS E  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9920)
  covalent geometry    : angle       0.60325 (13509)
  SS BOND              : bond        0.00457 (   15)
  SS BOND              : angle       1.14941 (   30)
  hydrogen bonds       : bond        0.02921 (  278)
  hydrogen bonds       : angle       5.84554 (  729)
  link_BETA1-4         : bond        0.00327 (    4)
  link_BETA1-4         : angle       1.14486 (   12)
  link_NAG-ASN         : bond        0.00295 (    9)
  link_NAG-ASN         : angle       1.63932 (   27)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  574 ASP cc_start: 0.7377 (p0) cc_final: 0.6951 (p0)
REVERT: C   69 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6807 (t-90)
REVERT: C  220 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7613 (t80)
REVERT: C  449 TYR cc_start: 0.8310 (m-10) cc_final: 0.7434 (t80)
REVERT: C  559 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6195 (m-10)
REVERT: D   32 ASN cc_start: 0.9005 (t0) cc_final: 0.8717 (t0)
REVERT: D   62 ASP cc_start: 0.8121 (t0) cc_final: 0.7829 (t0)
REVERT: D  108 HIS cc_start: 0.8172 (t-90) cc_final: 0.7914 (t-90)
REVERT: D  159 ASP cc_start: 0.8423 (m-30) cc_final: 0.7998 (t0)
REVERT: E   33 ASN cc_start: 0.8515 (p0) cc_final: 0.8134 (p0)
REVERT: E  190 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7305 (mmm160)
  outliers start: 27
  outliers final: 21
  residues processed: 122
  average time/residue: 0.0972
  time to fit residues: 17.0828
Evaluate side-chains
  118 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain C residue   69 HIS
Chi-restraints excluded: chain C residue  220 PHE
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  156 LEU
Chi-restraints excluded: chain D residue  198 THR
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    6 GLN
Chi-restraints excluded: chain E residue   18 ILE
Chi-restraints excluded: chain E residue   19 THR
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   74 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  213 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0030
   chunk 113 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.100269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.071742 restraints weight = 28368.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.074211 restraints weight = 16003.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.074553 restraints weight = 9934.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.075621 restraints weight = 9700.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.075674 restraints weight = 8342.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9948  Z= 0.128
  Angle     :  0.612  10.201  13578  Z= 0.300
  Chirality :  0.046   0.298   1538
  Planarity :  0.004   0.063   1723
  Dihedral  :  5.595  53.049   1592
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 25.78 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    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 are not related in a simple way.
  whole: -0.97 (0.24), residues: 1191
  helix: -1.51 (0.57), residues: 86
  sheet: -0.28 (0.26), residues: 389
  loop : -0.69 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 355 
 TYR   0.019   0.001   TYR D 209 
 PHE   0.020   0.001   PHE C 392 
 TRP   0.013   0.001   TRP D  36 
 HIS   0.002   0.000   HIS D 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9920)
  covalent geometry    : angle       0.60613 (13509)
  SS BOND              : bond        0.00454 (   15)
  SS BOND              : angle       1.11925 (   30)
  hydrogen bonds       : bond        0.02869 (  278)
  hydrogen bonds       : angle       5.83228 (  729)
  link_BETA1-4         : bond        0.00363 (    4)
  link_BETA1-4         : angle       1.14126 (   12)
  link_NAG-ASN         : bond        0.00301 (    9)
  link_NAG-ASN         : angle       1.56538 (   27)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1968.68 seconds
wall clock time: 34 minutes 49.87 seconds (2089.87 seconds total)