Starting phenix.real_space_refine
on Wed Mar  4 04:02:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f23_31426/03_2026/7f23_31426.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f23_31426/03_2026/7f23_31426.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f23_31426/03_2026/7f23_31426.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f23_31426/03_2026/7f23_31426.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f23_31426/03_2026/7f23_31426.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f23_31426/03_2026/7f23_31426.cif"
  }
  resolution = 3.58
  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=   0.003 sd=   0.090
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3063 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      53      5.16       5
     C    5196      2.51       5
     N    1440      2.21       5
     O    1519      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8211
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "F"
      Number of atoms: 2197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2197
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 9, 'TRANS': 266}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1937
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 2629
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 2624
    Chain: "E"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 434
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "F"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'LDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASP B  27 " occ=0.45
      ... (14 atoms not shown)
      pdb=" OD2BASP B  27 " occ=0.55
  Time building chain proxies: 2.34, per 1000 atoms: 0.28
  Number of scatterers: 8211
  At special positions: 0
  Unit cell: (84.786, 95.656, 126.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      53     16.00
     P       3     15.00
     O    1519      8.00
     N    1440      7.00
     C    5196      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " distance=2.05

  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
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 268.4 milliseconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      43.8% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'F' and resid 20 through 51
    Processing helix  chain 'F' and resid 58 through 88
      Proline residue:  F  79  - end of helix
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 4.325A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR F 108 " --> pdb=" O   ILE F 104 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ILE F 111 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
    Processing helix  chain 'F' and resid 136 through 161
      Proline residue:  F 158  - end of helix
    Processing helix  chain 'F' and resid 191 through 203
    Processing helix  chain 'F' and resid 203 through 237
      removed outlier: 3.601A  pdb=" N   ALA F 208 " --> pdb=" O   TYR F 204 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 265 through 298
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.777A  pdb=" N   GLY F 320 " --> pdb=" O   PHE F 316 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   TRP F 321 " --> pdb=" O   VAL F 317 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 346
    Processing helix  chain 'A' and resid 13 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.773A  pdb=" N   PHE A 312 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.264A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.051A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.984A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.507A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.772A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'D' and resid 55 through 59
      removed outlier: 3.571A  pdb=" N   ASN D  59 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 9.365A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.487A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.690A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.904A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.866A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.645A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.783A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.361A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.127A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 4.817A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1251 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: 1.27

  Time building geometry restraints manager: 0.66 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: 2681
        1.34 -     1.46: 2060
        1.46 -     1.58: 3567
        1.58 -     1.71: 5
        1.71 -     1.83: 72
  Bond restraints: 8385
  Sorted by residual:
  bond pdb=" N   CYS F  96 "
       pdb=" CA  CYS F  96 "
    ideal  model  delta    sigma   weight residual
    1.458  1.427  0.030 1.33e-02 5.65e+03 5.13e+00
  bond pdb=" CA  SER F 110 "
       pdb=" C   SER F 110 "
    ideal  model  delta    sigma   weight residual
    1.525  1.498  0.027 1.25e-02 6.40e+03 4.68e+00
  bond pdb=" CB  TRP B  99 "
       pdb=" CG  TRP B  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.434  0.064 3.10e-02 1.04e+03 4.22e+00
  bond pdb=" CG  LEU F  66 "
       pdb=" CD1 LEU F  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.15e+00
  bond pdb=" C3  LDP F 501 "
       pdb=" C4  LDP F 501 "
    ideal  model  delta    sigma   weight residual
    1.400  1.361  0.039 2.00e-02 2.50e+03 3.87e+00
  ... (remaining 8380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 11016
        2.51 -     5.01: 312
        5.01 -     7.52: 33
        7.52 -    10.02: 9
       10.02 -    12.53: 1
  Bond angle restraints: 11371
  Sorted by residual:
  angle pdb=" CA  CYS E  99 "
        pdb=" CB  CYS E  99 "
        pdb=" SG  CYS E  99 "
      ideal   model   delta    sigma   weight residual
     114.40  126.93  -12.53 2.30e+00 1.89e-01 2.97e+01
  angle pdb=" C   LYS A 233 "
        pdb=" N   TRP A 234 "
        pdb=" CA  TRP A 234 "
      ideal   model   delta    sigma   weight residual
     121.58  113.52    8.06 1.95e+00 2.63e-01 1.71e+01
  angle pdb=" C   THR F 108 "
        pdb=" N   ALA F 109 "
        pdb=" CA  ALA F 109 "
      ideal   model   delta    sigma   weight residual
     120.72  114.50    6.22 1.67e+00 3.59e-01 1.39e+01
  angle pdb=" C   SER B 334 "
        pdb=" CA  SER B 334 "
        pdb=" CB  SER B 334 "
      ideal   model   delta    sigma   weight residual
     111.63  106.58    5.05 1.36e+00 5.41e-01 1.38e+01
  angle pdb=" C   GLY B 131 "
        pdb=" N   ASN B 132 "
        pdb=" CA  ASN B 132 "
      ideal   model   delta    sigma   weight residual
     122.81  128.33   -5.52 1.57e+00 4.06e-01 1.24e+01
  ... (remaining 11366 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.60: 4895
       34.60 -    69.20: 87
       69.20 -   103.80: 4
      103.80 -   138.40: 1
      138.40 -   173.00: 2
  Dihedral angle restraints: 4989
    sinusoidal: 1958
      harmonic: 3031
  Sorted by residual:
  dihedral pdb=" CB  CYS E  99 "
           pdb=" SG  CYS E  99 "
           pdb=" SG  CYS E 107 "
           pdb=" CB  CYS E 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -18.21  -67.79     1      1.00e+01 1.00e-02 5.97e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -117.73 -173.00     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -36.16  140.75     1      2.00e+01 2.50e-03 4.26e+01
  ... (remaining 4986 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 956
       0.062 -    0.125: 272
       0.125 -    0.187: 48
       0.187 -    0.250: 1
       0.250 -    0.312: 1
  Chirality restraints: 1278
  Sorted by residual:
  chirality pdb=" CA  CYS E  99 "
            pdb=" N   CYS E  99 "
            pdb=" C   CYS E  99 "
            pdb=" CB  CYS E  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  PRO F 206 "
            pdb=" N   PRO F 206 "
            pdb=" C   PRO F 206 "
            pdb=" CB  PRO F 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.53e-01
  chirality pdb=" CA  PHE A 222 "
            pdb=" N   PHE A 222 "
            pdb=" C   PHE A 222 "
            pdb=" CB  PHE A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.58e-01
  ... (remaining 1275 not shown)

  Planarity restraints: 1444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F 109 "   -0.043 2.00e-02 2.50e+03   8.57e-02 7.34e+01
        pdb=" C   ALA F 109 "    0.148 2.00e-02 2.50e+03
        pdb=" O   ALA F 109 "   -0.054 2.00e-02 2.50e+03
        pdb=" N   SER F 110 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER F  94 "   -0.030 2.00e-02 2.50e+03   6.06e-02 3.68e+01
        pdb=" C   SER F  94 "    0.105 2.00e-02 2.50e+03
        pdb=" O   SER F  94 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   PHE F  95 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 347 "   -0.021 2.00e-02 2.50e+03   4.26e-02 1.81e+01
        pdb=" C   ARG A 347 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ARG A 347 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ILE A 348 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1441 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 216
        2.65 -     3.21: 8278
        3.21 -     3.77: 13082
        3.77 -     4.34: 17654
        4.34 -     4.90: 29033
  Nonbonded interactions: 68263
  Sorted by model distance:
  nonbonded pdb=" OG  SER F  65 "
            pdb=" ND2 ASN F 113 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD2 ASP B 333 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER A  54 "
            pdb=" O1G GTP A 401 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" OG1 THR A  55 "
            pdb=" O1A GTP A 401 "
     model   vdw
     2.164 3.040
  ... (remaining 68258 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
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      :  0.010   0.068   8388  Z= 0.468
  Angle     :  1.013  12.527  11377  Z= 0.575
  Chirality :  0.057   0.312   1278
  Planarity :  0.007   0.086   1444
  Dihedral  : 15.075 172.997   3016
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.99 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.23), residues: 1025
  helix: -1.68 (0.21), residues: 416
  sheet: -1.41 (0.30), residues: 245
  loop : -1.74 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 226 
 TYR   0.018   0.002   TYR E  95 
 PHE   0.032   0.003   PHE F 333 
 TRP   0.016   0.002   TRP F  99 
 HIS   0.014   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.01034 ( 8385)
  covalent geometry    : angle       1.00598 (11371)
  SS BOND              : bond        0.01128 (    3)
  SS BOND              : angle       5.23469 (    6)
  hydrogen bonds       : bond        0.12964 (  435)
  hydrogen bonds       : angle       6.83344 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   86 ILE cc_start: 0.8784 (mm) cc_final: 0.8539 (mt)
REVERT: F  194 TYR cc_start: 0.8868 (t80) cc_final: 0.8659 (t80)
REVERT: A   20 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8068 (mtt-85)
REVERT: A   33 ASP cc_start: 0.8447 (t0) cc_final: 0.8115 (t0)
REVERT: A   35 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: B  214 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6756 (ttp-170)
REVERT: B  269 ILE cc_start: 0.9095 (mt) cc_final: 0.8793 (mm)
REVERT: E   29 PHE cc_start: 0.9027 (t80) cc_final: 0.8697 (t80)
REVERT: E   80 TYR cc_start: 0.7366 (m-80) cc_final: 0.7082 (m-80)
REVERT: E   82 GLN cc_start: 0.7631 (tp40) cc_final: 0.7294 (tp40)
REVERT: E   83 MET cc_start: 0.7743 (ptp) cc_final: 0.7523 (ptp)
REVERT: D   47 GLU cc_start: 0.7750 (pm20) cc_final: 0.6942 (pm20)
  outliers start: 2
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0964
  time to fit residues: 27.0468
Evaluate side-chains
  160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:   30.0000
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.1380

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

Flipped N/Q/H residues before XYZ refinement:
F  41 ASN
F 113 ASN
F 164 HIS
F 222 GLN
A  14 ASN
A 267 GLN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B 119 ASN
B 266 HIS
E  13 GLN
E  77 ASN
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.160435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.120201 restraints weight = 34556.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.123488 restraints weight = 15157.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.124527 restraints weight = 10357.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.127220 restraints weight = 6736.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.127735 restraints weight = 5589.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8388  Z= 0.161
  Angle     :  0.655  12.203  11377  Z= 0.341
  Chirality :  0.046   0.173   1278
  Planarity :  0.004   0.043   1444
  Dihedral  :  9.554 178.044   1155
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.29 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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: -0.59 (0.25), residues: 1025
  helix:  0.40 (0.24), residues: 415
  sheet: -0.83 (0.33), residues: 216
  loop : -0.81 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 105 
 TYR   0.014   0.001   TYR F 122 
 PHE   0.016   0.001   PHE E 108 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8385)
  covalent geometry    : angle       0.64809 (11371)
  SS BOND              : bond        0.00530 (    3)
  SS BOND              : angle       4.27616 (    6)
  hydrogen bonds       : bond        0.04945 (  435)
  hydrogen bonds       : angle       5.09162 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  211 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7465 (mt)
REVERT: F  271 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8923 (mm)
REVERT: F  333 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7910 (m-10)
REVERT: A   33 ASP cc_start: 0.8436 (t0) cc_final: 0.8076 (t0)
REVERT: A  249 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7614 (p0)
REVERT: A  356 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8181 (mtm180)
REVERT: B   46 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7038 (mtm110)
REVERT: B  211 TRP cc_start: 0.7759 (m100) cc_final: 0.7455 (m100)
REVERT: B  214 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6899 (ptp-170)
REVERT: B  289 TYR cc_start: 0.8994 (m-80) cc_final: 0.8771 (m-80)
REVERT: E   29 PHE cc_start: 0.8953 (t80) cc_final: 0.8751 (t80)
REVERT: E   82 GLN cc_start: 0.7618 (tp40) cc_final: 0.7295 (tp40)
REVERT: D   47 GLU cc_start: 0.8079 (pm20) cc_final: 0.7744 (pm20)
  outliers start: 20
  outliers final: 11
  residues processed: 212
  average time/residue: 0.0905
  time to fit residues: 26.0592
Evaluate side-chains
  181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  211 ILE
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  290 ILE
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 87 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 26 optimal weight:    0.6980
   chunk 28 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** 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 = 0.4038 r_free = 0.4038 target = 0.161676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111762 restraints weight = 38070.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.117862 restraints weight = 12702.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.121474 restraints weight = 6900.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.121682 restraints weight = 6073.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.121499 restraints weight = 5411.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8388  Z= 0.187
  Angle     :  0.649  11.585  11377  Z= 0.338
  Chirality :  0.045   0.193   1278
  Planarity :  0.004   0.040   1444
  Dihedral  :  9.515 179.597   1155
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.35 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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:  0.04 (0.26), residues: 1025
  helix:  1.01 (0.25), residues: 424
  sheet: -0.59 (0.33), residues: 218
  loop : -0.58 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  19 
 TYR   0.013   0.001   TYR F 194 
 PHE   0.021   0.002   PHE B 235 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.009   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 8385)
  covalent geometry    : angle       0.64161 (11371)
  SS BOND              : bond        0.00554 (    3)
  SS BOND              : angle       4.43195 (    6)
  hydrogen bonds       : bond        0.04792 (  435)
  hydrogen bonds       : angle       4.88467 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 171
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: F   78 MET cc_start: 0.7657 (mmm) cc_final: 0.7369 (mmm)
REVERT: F  271 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8852 (mm)
REVERT: F  333 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7915 (m-10)
REVERT: A   33 ASP cc_start: 0.8436 (t0) cc_final: 0.8035 (t0)
REVERT: A  249 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7633 (p0)
REVERT: A  253 TYR cc_start: 0.7473 (m-80) cc_final: 0.6755 (m-80)
REVERT: A  356 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8223 (mtm180)
REVERT: B   45 MET cc_start: 0.8661 (mtm) cc_final: 0.8413 (mtm)
REVERT: B  214 ARG cc_start: 0.7192 (mtm180) cc_final: 0.6943 (ptp-170)
REVERT: B  217 MET cc_start: 0.6815 (ptm) cc_final: 0.6596 (ptm)
REVERT: B  234 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8204 (t80)
REVERT: B  289 TYR cc_start: 0.9096 (m-80) cc_final: 0.8858 (m-80)
REVERT: B  297 TRP cc_start: 0.8135 (m100) cc_final: 0.7900 (m-10)
REVERT: E   29 PHE cc_start: 0.9139 (t80) cc_final: 0.8738 (t80)
REVERT: E   82 GLN cc_start: 0.7710 (tp40) cc_final: 0.7324 (tp40)
REVERT: E   98 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7906 (tmm-80)
REVERT: D   47 GLU cc_start: 0.8138 (pm20) cc_final: 0.7695 (pm20)
  outliers start: 35
  outliers final: 16
  residues processed: 194
  average time/residue: 0.0829
  time to fit residues: 21.9068
Evaluate side-chains
  178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  132 GLU
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   50 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
B 295 ASN
E  35 ASN
** E  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.163500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.120939 restraints weight = 31185.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.123573 restraints weight = 12580.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.124844 restraints weight = 9465.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.127470 restraints weight = 6467.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127954 restraints weight = 5515.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8388  Z= 0.140
  Angle     :  0.602  11.154  11377  Z= 0.311
  Chirality :  0.044   0.204   1278
  Planarity :  0.004   0.043   1444
  Dihedral  :  9.407 179.234   1155
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.84 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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:  0.34 (0.27), residues: 1025
  helix:  1.33 (0.26), residues: 423
  sheet: -0.36 (0.34), residues: 216
  loop : -0.54 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  19 
 TYR   0.023   0.001   TYR F 194 
 PHE   0.021   0.001   PHE B 235 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.010   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8385)
  covalent geometry    : angle       0.59573 (11371)
  SS BOND              : bond        0.00624 (    3)
  SS BOND              : angle       3.78813 (    6)
  hydrogen bonds       : bond        0.04316 (  435)
  hydrogen bonds       : angle       4.62817 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  160 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7876 (tm-30)
REVERT: F  271 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8824 (mm)
REVERT: F  333 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7796 (m-10)
REVERT: A   33 ASP cc_start: 0.8321 (t0) cc_final: 0.7903 (t0)
REVERT: A  249 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7423 (p0)
REVERT: B  211 TRP cc_start: 0.7601 (m100) cc_final: 0.7260 (m100)
REVERT: B  214 ARG cc_start: 0.7177 (mtm180) cc_final: 0.6945 (ptp-170)
REVERT: B  217 MET cc_start: 0.6912 (ptm) cc_final: 0.6704 (ptm)
REVERT: B  235 PHE cc_start: 0.8874 (t80) cc_final: 0.8521 (t80)
REVERT: E    4 LEU cc_start: 0.7970 (mt) cc_final: 0.7441 (tp)
REVERT: E   33 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7785 (ptmt)
REVERT: E   43 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7259 (ptpt)
REVERT: E  106 ASP cc_start: 0.7935 (p0) cc_final: 0.7648 (p0)
REVERT: D   47 GLU cc_start: 0.8142 (pm20) cc_final: 0.7699 (pm20)
  outliers start: 28
  outliers final: 20
  residues processed: 198
  average time/residue: 0.0920
  time to fit residues: 24.3634
Evaluate side-chains
  187 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  185 ASN
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   20 LEU
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Chi-restraints excluded: chain D residue   50 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 67 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 96 optimal weight:   30.0000
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
E  35 ASN
E  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.164162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.117595 restraints weight = 34427.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.121783 restraints weight = 12055.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.126378 restraints weight = 7255.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.126842 restraints weight = 5463.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126593 restraints weight = 4975.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8388  Z= 0.137
  Angle     :  0.610  10.465  11377  Z= 0.312
  Chirality :  0.044   0.222   1278
  Planarity :  0.004   0.045   1444
  Dihedral  :  9.343 179.668   1155
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 22.42 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.27), residues: 1025
  helix:  1.44 (0.26), residues: 422
  sheet: -0.18 (0.35), residues: 216
  loop : -0.42 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  52 
 TYR   0.021   0.001   TYR F 194 
 PHE   0.016   0.001   PHE B 235 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8385)
  covalent geometry    : angle       0.60444 (11371)
  SS BOND              : bond        0.00405 (    3)
  SS BOND              : angle       3.64465 (    6)
  hydrogen bonds       : bond        0.04171 (  435)
  hydrogen bonds       : angle       4.50609 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: F   78 MET cc_start: 0.7470 (mmm) cc_final: 0.7261 (mmt)
REVERT: F  160 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: F  161 LEU cc_start: 0.8455 (mp) cc_final: 0.7941 (mp)
REVERT: F  214 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6929 (m-10)
REVERT: F  271 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8797 (mt)
REVERT: F  333 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7839 (m-10)
REVERT: A   33 ASP cc_start: 0.8277 (t0) cc_final: 0.7850 (t0)
REVERT: A  249 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7375 (p0)
REVERT: B  211 TRP cc_start: 0.7682 (m100) cc_final: 0.7312 (m100)
REVERT: B  214 ARG cc_start: 0.7160 (mtm180) cc_final: 0.6883 (ttp-170)
REVERT: B  235 PHE cc_start: 0.8925 (t80) cc_final: 0.8599 (t80)
REVERT: B  254 ASP cc_start: 0.8354 (t70) cc_final: 0.8061 (t0)
REVERT: B  262 MET cc_start: 0.6603 (ttm) cc_final: 0.6398 (ttm)
REVERT: E    4 LEU cc_start: 0.8023 (mt) cc_final: 0.7461 (tp)
REVERT: E   33 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7614 (ptmt)
REVERT: E   43 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7356 (ptpt)
REVERT: E   82 GLN cc_start: 0.7559 (tp40) cc_final: 0.7280 (tp-100)
REVERT: E  106 ASP cc_start: 0.8129 (p0) cc_final: 0.7877 (p0)
REVERT: D   47 GLU cc_start: 0.8117 (pm20) cc_final: 0.7604 (pm20)
  outliers start: 34
  outliers final: 22
  residues processed: 188
  average time/residue: 0.0811
  time to fit residues: 21.1115
Evaluate side-chains
  190 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 266 HIS
** E  53 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 = 0.4070 r_free = 0.4070 target = 0.164086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.117055 restraints weight = 38655.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.122332 restraints weight = 12642.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.124480 restraints weight = 7727.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125624 restraints weight = 5947.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.125790 restraints weight = 5179.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8388  Z= 0.143
  Angle     :  0.623  11.104  11377  Z= 0.315
  Chirality :  0.044   0.230   1278
  Planarity :  0.004   0.046   1444
  Dihedral  :  9.328 179.622   1155
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 23.10 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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:  0.62 (0.27), residues: 1025
  helix:  1.53 (0.26), residues: 422
  sheet:  0.03 (0.36), residues: 203
  loop : -0.52 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  52 
 TYR   0.022   0.001   TYR F 194 
 PHE   0.017   0.001   PHE B 235 
 TRP   0.015   0.001   TRP A 281 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8385)
  covalent geometry    : angle       0.61763 (11371)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       3.50672 (    6)
  hydrogen bonds       : bond        0.04131 (  435)
  hydrogen bonds       : angle       4.46325 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  160 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7928 (tm-30)
REVERT: F  161 LEU cc_start: 0.8467 (mp) cc_final: 0.8020 (mp)
REVERT: F  214 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6928 (m-10)
REVERT: F  271 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8795 (mt)
REVERT: F  333 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7882 (m-10)
REVERT: A   33 ASP cc_start: 0.8338 (t0) cc_final: 0.7947 (t0)
REVERT: A  249 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7429 (p0)
REVERT: B  211 TRP cc_start: 0.7682 (m100) cc_final: 0.7285 (m100)
REVERT: B  235 PHE cc_start: 0.8972 (t80) cc_final: 0.8630 (t80)
REVERT: B  254 ASP cc_start: 0.8420 (t70) cc_final: 0.8084 (t0)
REVERT: B  262 MET cc_start: 0.6628 (ttm) cc_final: 0.6379 (ttm)
REVERT: E    4 LEU cc_start: 0.7962 (mt) cc_final: 0.7394 (tp)
REVERT: E    6 GLU cc_start: 0.6258 (pm20) cc_final: 0.6037 (pm20)
REVERT: E   33 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7687 (ptmt)
REVERT: E   43 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7387 (ptpt)
REVERT: E   77 ASN cc_start: 0.7236 (t0) cc_final: 0.6996 (t0)
REVERT: E  106 ASP cc_start: 0.8084 (p0) cc_final: 0.7751 (p0)
REVERT: D   47 GLU cc_start: 0.8068 (pm20) cc_final: 0.7686 (pm20)
  outliers start: 33
  outliers final: 28
  residues processed: 191
  average time/residue: 0.0871
  time to fit residues: 22.8915
Evaluate side-chains
  193 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 92 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
** D  59 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.158984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.111368 restraints weight = 44082.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116630 restraints weight = 13278.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.119923 restraints weight = 7516.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.120499 restraints weight = 5944.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.120490 restraints weight = 5172.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8388  Z= 0.195
  Angle     :  0.655  11.065  11377  Z= 0.334
  Chirality :  0.045   0.246   1278
  Planarity :  0.004   0.045   1444
  Dihedral  :  9.384 179.917   1155
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 24.69 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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:  0.62 (0.27), residues: 1025
  helix:  1.60 (0.25), residues: 414
  sheet: -0.02 (0.35), residues: 205
  loop : -0.53 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  38 
 TYR   0.024   0.001   TYR F 194 
 PHE   0.019   0.002   PHE E 108 
 TRP   0.018   0.002   TRP A 281 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8385)
  covalent geometry    : angle       0.64962 (11371)
  SS BOND              : bond        0.00442 (    3)
  SS BOND              : angle       3.78649 (    6)
  hydrogen bonds       : bond        0.04391 (  435)
  hydrogen bonds       : angle       4.58246 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 162
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  161 LEU cc_start: 0.8517 (mp) cc_final: 0.7866 (mp)
REVERT: F  214 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7081 (m-80)
REVERT: F  271 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8809 (mm)
REVERT: F  333 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7905 (m-10)
REVERT: A  249 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7376 (p0)
REVERT: B  211 TRP cc_start: 0.7786 (m100) cc_final: 0.7457 (m100)
REVERT: B  234 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7685 (t80)
REVERT: B  235 PHE cc_start: 0.8926 (t80) cc_final: 0.8488 (t80)
REVERT: B  254 ASP cc_start: 0.8444 (t70) cc_final: 0.8121 (t0)
REVERT: B  262 MET cc_start: 0.6749 (ttm) cc_final: 0.6364 (ttm)
REVERT: E    4 LEU cc_start: 0.7957 (mt) cc_final: 0.7746 (mt)
REVERT: E  106 ASP cc_start: 0.8136 (p0) cc_final: 0.7870 (p0)
REVERT: D   47 GLU cc_start: 0.8066 (pm20) cc_final: 0.7636 (pm20)
  outliers start: 37
  outliers final: 30
  residues processed: 184
  average time/residue: 0.0774
  time to fit residues: 19.8655
Evaluate side-chains
  189 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  112 LEU
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0060
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.1400

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
** E  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
** D  59 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.161594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.114794 restraints weight = 47157.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120559 restraints weight = 13426.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.123550 restraints weight = 7441.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.124542 restraints weight = 5680.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124484 restraints weight = 5084.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8388  Z= 0.138
  Angle     :  0.626  10.881  11377  Z= 0.319
  Chirality :  0.044   0.259   1278
  Planarity :  0.004   0.047   1444
  Dihedral  :  9.305 179.124   1155
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 25.48 %
    Favored  : 70.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.27), residues: 1025
  helix:  1.72 (0.26), residues: 412
  sheet: -0.02 (0.35), residues: 205
  loop : -0.51 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  38 
 TYR   0.025   0.001   TYR F 194 
 PHE   0.016   0.001   PHE B 235 
 TRP   0.017   0.001   TRP A 281 
 HIS   0.006   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8385)
  covalent geometry    : angle       0.62178 (11371)
  SS BOND              : bond        0.00366 (    3)
  SS BOND              : angle       3.30088 (    6)
  hydrogen bonds       : bond        0.04065 (  435)
  hydrogen bonds       : angle       4.46062 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   76 LEU cc_start: 0.8315 (mp) cc_final: 0.8013 (tt)
REVERT: F  214 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6873 (m-10)
REVERT: F  271 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8794 (mt)
REVERT: F  333 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7859 (m-10)
REVERT: A  249 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7513 (p0)
REVERT: B  188 MET cc_start: 0.7651 (mmt) cc_final: 0.7220 (mtt)
REVERT: B  211 TRP cc_start: 0.7693 (m100) cc_final: 0.7345 (m100)
REVERT: B  234 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7755 (t80)
REVERT: B  235 PHE cc_start: 0.8946 (t80) cc_final: 0.8559 (t80)
REVERT: B  254 ASP cc_start: 0.8444 (t70) cc_final: 0.8118 (t0)
REVERT: B  264 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7536 (m-80)
REVERT: E    4 LEU cc_start: 0.7853 (mt) cc_final: 0.7651 (mt)
REVERT: E   33 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7824 (ptpt)
REVERT: E   82 GLN cc_start: 0.7508 (tp40) cc_final: 0.7254 (tp40)
REVERT: E  106 ASP cc_start: 0.8157 (p0) cc_final: 0.7871 (p0)
REVERT: D   47 GLU cc_start: 0.8006 (pm20) cc_final: 0.7715 (pm20)
  outliers start: 33
  outliers final: 22
  residues processed: 188
  average time/residue: 0.0794
  time to fit residues: 20.9428
Evaluate side-chains
  192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  145 SER
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   74 ASN
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
** D  59 ASN ** 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 = 0.3967 r_free = 0.3967 target = 0.155610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107356 restraints weight = 37194.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.113031 restraints weight = 12896.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115220 restraints weight = 6936.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116060 restraints weight = 6223.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.115983 restraints weight = 5602.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   8388  Z= 0.287
  Angle     :  0.728  11.836  11377  Z= 0.375
  Chirality :  0.047   0.266   1278
  Planarity :  0.004   0.050   1444
  Dihedral  :  9.525 178.854   1155
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 26.39 %
    Favored  : 69.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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:  0.41 (0.27), residues: 1025
  helix:  1.38 (0.25), residues: 411
  sheet: -0.30 (0.34), residues: 217
  loop : -0.46 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  38 
 TYR   0.027   0.002   TYR F 194 
 PHE   0.022   0.002   PHE E 108 
 TRP   0.025   0.002   TRP A 281 
 HIS   0.009   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 ( 8385)
  covalent geometry    : angle       0.72270 (11371)
  SS BOND              : bond        0.00473 (    3)
  SS BOND              : angle       3.79588 (    6)
  hydrogen bonds       : bond        0.04883 (  435)
  hydrogen bonds       : angle       4.78111 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 160
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   50 ARG cc_start: 0.5506 (mtt180) cc_final: 0.4469 (tpt170)
REVERT: F  214 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7115 (m-80)
REVERT: F  271 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8818 (mm)
REVERT: F  333 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7941 (m-10)
REVERT: A   60 MET cc_start: 0.8428 (mmm) cc_final: 0.8007 (mmm)
REVERT: A  220 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7241 (t70)
REVERT: A  249 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7643 (p0)
REVERT: B  211 TRP cc_start: 0.7992 (m100) cc_final: 0.7718 (m100)
REVERT: B  234 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8039 (t80)
REVERT: B  235 PHE cc_start: 0.9026 (t80) cc_final: 0.8671 (t80)
REVERT: B  254 ASP cc_start: 0.8454 (t70) cc_final: 0.8105 (t0)
REVERT: B  264 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8079 (m-80)
REVERT: E   77 ASN cc_start: 0.7607 (t0) cc_final: 0.7303 (t0)
REVERT: E   82 GLN cc_start: 0.7452 (tp40) cc_final: 0.7245 (tp40)
REVERT: D   47 GLU cc_start: 0.8078 (pm20) cc_final: 0.7811 (pm20)
  outliers start: 35
  outliers final: 27
  residues processed: 182
  average time/residue: 0.0785
  time to fit residues: 19.8831
Evaluate side-chains
  188 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 THR
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  132 GLU
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  325 SER
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   33 LYS
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   74 ASN
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 100 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** 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 = 0.4019 r_free = 0.4019 target = 0.160130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.117847 restraints weight = 30336.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.120311 restraints weight = 11681.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.121357 restraints weight = 8382.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.125272 restraints weight = 6497.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.125693 restraints weight = 4980.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8388  Z= 0.147
  Angle     :  0.644  12.089  11377  Z= 0.327
  Chirality :  0.044   0.274   1278
  Planarity :  0.004   0.059   1444
  Dihedral  :  9.444 179.580   1155
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 26.61 %
    Favored  : 69.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.27), residues: 1025
  helix:  1.65 (0.26), residues: 411
  sheet: -0.10 (0.35), residues: 206
  loop : -0.47 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  38 
 TYR   0.027   0.001   TYR F 194 
 PHE   0.016   0.001   PHE B 235 
 TRP   0.019   0.001   TRP A 281 
 HIS   0.010   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8385)
  covalent geometry    : angle       0.63949 (11371)
  SS BOND              : bond        0.00347 (    3)
  SS BOND              : angle       3.39523 (    6)
  hydrogen bonds       : bond        0.04235 (  435)
  hydrogen bonds       : angle       4.55650 ( 1251)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 165
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  214 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.6785 (m-80)
REVERT: F  271 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8827 (mt)
REVERT: F  333 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7915 (m-10)
REVERT: A   60 MET cc_start: 0.8379 (mmm) cc_final: 0.8119 (mmm)
REVERT: A  220 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7624 (t-170)
REVERT: A  249 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7477 (p0)
REVERT: B  211 TRP cc_start: 0.7762 (m100) cc_final: 0.7452 (m100)
REVERT: B  214 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7790 (ttp-170)
REVERT: B  217 MET cc_start: 0.6393 (ptm) cc_final: 0.5955 (ppp)
REVERT: B  234 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7799 (t80)
REVERT: B  235 PHE cc_start: 0.8927 (t80) cc_final: 0.8643 (t80)
REVERT: B  254 ASP cc_start: 0.8431 (t70) cc_final: 0.8135 (t0)
REVERT: B  264 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7946 (m-80)
REVERT: E   77 ASN cc_start: 0.7535 (t0) cc_final: 0.7219 (t0)
REVERT: E   82 GLN cc_start: 0.7479 (tp40) cc_final: 0.7244 (tp40)
REVERT: D   47 GLU cc_start: 0.7946 (pm20) cc_final: 0.7693 (pm20)
  outliers start: 33
  outliers final: 24
  residues processed: 182
  average time/residue: 0.0759
  time to fit residues: 19.6169
Evaluate side-chains
  193 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 161
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue   68 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue  132 GLU
Chi-restraints excluded: chain F residue  146 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  213 THR
Chi-restraints excluded: chain F residue  214 TYR
Chi-restraints excluded: chain F residue  271 LEU
Chi-restraints excluded: chain F residue  323 ASN
Chi-restraints excluded: chain F residue  325 SER
Chi-restraints excluded: chain F residue  329 ILE
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain E residue   74 ASN
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain D residue   44 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 87 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.162068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.115792 restraints weight = 38709.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.120864 restraints weight = 12255.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124849 restraints weight = 7095.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125243 restraints weight = 5492.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125270 restraints weight = 4946.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8388  Z= 0.130
  Angle     :  0.628  11.013  11377  Z= 0.319
  Chirality :  0.044   0.282   1278
  Planarity :  0.004   0.065   1444
  Dihedral  :  9.338 178.234   1155
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 27.18 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.27), residues: 1025
  helix:  1.77 (0.26), residues: 412
  sheet: -0.18 (0.34), residues: 212
  loop : -0.45 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  38 
 TYR   0.025   0.001   TYR F 194 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.016   0.001   TRP A 281 
 HIS   0.010   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8385)
  covalent geometry    : angle       0.62382 (11371)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       3.04083 (    6)
  hydrogen bonds       : bond        0.03996 (  435)
  hydrogen bonds       : angle       4.46085 ( 1251)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1517.02 seconds
wall clock time: 26 minutes 51.16 seconds (1611.16 seconds total)