Starting phenix.real_space_refine
on Tue Mar  3 22:34:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vqx_32095/03_2026/7vqx_32095_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vqx_32095/03_2026/7vqx_32095.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vqx_32095/03_2026/7vqx_32095_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vqx_32095/03_2026/7vqx_32095_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vqx_32095/03_2026/7vqx_32095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vqx_32095/03_2026/7vqx_32095.map"
  }
  resolution = 2.74
  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=  -0.001 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5735      2.51       5
     N    1566      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  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: 9049
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1962
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2598
          Classifications: {'peptide': 340}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "L"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 221
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 967
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2877
          Classifications: {'peptide': 361}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 14, 'TRANS': 346}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 2.10, per 1000 atoms: 0.23
  Number of scatterers: 9049
  At special positions: 0
  Unit cell: (76.041, 101.745, 168.147, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1688      8.00
     N    1566      7.00
     C    5735      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  38 " - pdb=" SG  CYS R  61 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  52 " - pdb=" SG  CYS R  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  75 " - pdb=" SG  CYS R 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 202 " - pdb=" SG  CYS R 271 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 337.8 milliseconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      41.8% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 4.657A  pdb=" N   ASN A  14 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.500A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.568A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.748A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.936A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.714A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'L' and resid 2 through 27
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.740A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 26 through 43
      removed outlier: 3.641A  pdb=" N   GLU R  30 " --> pdb=" O   ARG R  26 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 83
      removed outlier: 5.183A  pdb=" N   ASN R  81 " --> pdb=" O   VAL R  78 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR R  83 " --> pdb=" O   SER R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 110
    Processing helix  chain 'R' and resid 115 through 117
      No H-bonds generated for 'chain 'R' and resid 115 through 117'
    Processing helix  chain 'R' and resid 118 through 151
      removed outlier: 4.451A  pdb=" N   PHE R 122 " --> pdb=" O   SER R 118 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   THR R 131 " --> pdb=" O   LYS R 127 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   THR R 143 " --> pdb=" O   MET R 139 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE R 151 " --> pdb=" O   ILE R 147 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 155
    Processing helix  chain 'R' and resid 156 through 184
    Processing helix  chain 'R' and resid 195 through 233
      removed outlier: 4.282A  pdb=" N   TRP R 199 " --> pdb=" O   GLN R 195 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLY R 224 " --> pdb=" O   LEU R 220 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 240 through 266
      removed outlier: 4.245A  pdb=" N   LEU R 251 " --> pdb=" O   ILE R 247 " (cutoff:3.500A)
      Proline residue:  R 252  - end of helix
    Processing helix  chain 'R' and resid 277 through 312
      removed outlier: 3.779A  pdb=" N   TRP R 281 " --> pdb=" O   HIS R 277 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE R 284 " --> pdb=" O   PRO R 280 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      removed outlier: 3.508A  pdb=" N   SER R 312 " --> pdb=" O   GLN R 308 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 323 through 338
      Proline residue:  R 335  - end of helix
    Processing helix  chain 'R' and resid 341 through 347
      removed outlier: 3.911A  pdb=" N   VAL R 346 " --> pdb=" O   MET R 342 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   PHE R 347 " --> pdb=" O   VAL R 343 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 353 through 365
      removed outlier: 3.791A  pdb=" N   CYS R 362 " --> pdb=" O   LEU R 358 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 366 through 377
    Processing helix  chain 'R' and resid 379 through 393
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.365A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51
      removed outlier: 5.382A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.629A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.780A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.545A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.301A  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: 6.874A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.576A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.872A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
      removed outlier: 3.574A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 7.009A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 70 through 74

    451 hydrogen bonds defined for protein.
    1302 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: 1.53

  Time building geometry restraints manager: 0.96 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: 2955
        1.34 -     1.46: 2043
        1.46 -     1.58: 4162
        1.58 -     1.70: 0
        1.70 -     1.81: 79
  Bond restraints: 9239
  Sorted by residual:
  bond pdb=" CB  CYS B 103 "
       pdb=" SG  CYS B 103 "
    ideal  model  delta    sigma   weight residual
    1.808  1.761  0.047 3.30e-02 9.18e+02 2.01e+00
  bond pdb=" C   ARG N  98 "
       pdb=" N   CYS N  99 "
    ideal  model  delta    sigma   weight residual
    1.330  1.311  0.019 1.47e-02 4.63e+03 1.71e+00
  bond pdb=" CB  CYS N  99 "
       pdb=" SG  CYS N  99 "
    ideal  model  delta    sigma   weight residual
    1.808  1.769  0.039 3.30e-02 9.18e+02 1.43e+00
  bond pdb=" CB  VAL N 110 "
       pdb=" CG1 VAL N 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CB  ARG A 232 "
       pdb=" CG  ARG A 232 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.14e+00
  ... (remaining 9234 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 12154
        1.38 -     2.76: 296
        2.76 -     4.14: 50
        4.14 -     5.52: 14
        5.52 -     6.90: 2
  Bond angle restraints: 12516
  Sorted by residual:
  angle pdb=" C   ILE B  58 "
        pdb=" N   TYR B  59 "
        pdb=" CA  TYR B  59 "
      ideal   model   delta    sigma   weight residual
     122.11  117.23    4.88 1.64e+00 3.72e-01 8.84e+00
  angle pdb=" C   ILE R 286 "
        pdb=" CA  ILE R 286 "
        pdb=" CB  ILE R 286 "
      ideal   model   delta    sigma   weight residual
     114.00  110.95    3.05 1.31e+00 5.83e-01 5.41e+00
  angle pdb=" N   PHE N 108 "
        pdb=" CA  PHE N 108 "
        pdb=" C   PHE N 108 "
      ideal   model   delta    sigma   weight residual
     110.80  115.67   -4.87 2.13e+00 2.20e-01 5.24e+00
  angle pdb=" C   ARG R 285 "
        pdb=" N   ILE R 286 "
        pdb=" CA  ILE R 286 "
      ideal   model   delta    sigma   weight residual
     120.33  122.08   -1.75 8.00e-01 1.56e+00 4.80e+00
  angle pdb=" N   GLY B 216 "
        pdb=" CA  GLY B 216 "
        pdb=" C   GLY B 216 "
      ideal   model   delta    sigma   weight residual
     113.18  118.16   -4.98 2.37e+00 1.78e-01 4.42e+00
  ... (remaining 12511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 4952
       17.38 -    34.77: 455
       34.77 -    52.15: 77
       52.15 -    69.53: 12
       69.53 -    86.91: 16
  Dihedral angle restraints: 5512
    sinusoidal: 2172
      harmonic: 3340
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.30  -76.30     1      1.00e+01 1.00e-02 7.33e+01
  dihedral pdb=" CB  CYS R 202 "
           pdb=" SG  CYS R 202 "
           pdb=" SG  CYS R 271 "
           pdb=" CB  CYS R 271 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.70  -62.70     1      1.00e+01 1.00e-02 5.20e+01
  dihedral pdb=" CB  CYS R  38 "
           pdb=" SG  CYS R  38 "
           pdb=" SG  CYS R  61 "
           pdb=" CB  CYS R  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.10  -44.10     1      1.00e+01 1.00e-02 2.71e+01
  ... (remaining 5509 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 797
       0.029 -    0.058: 384
       0.058 -    0.087: 146
       0.087 -    0.116: 61
       0.116 -    0.145: 16
  Chirality restraints: 1404
  Sorted by residual:
  chirality pdb=" CA  ILE N  58 "
            pdb=" N   ILE N  58 "
            pdb=" C   ILE N  58 "
            pdb=" CB  ILE N  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  chirality pdb=" CA  ILE B 123 "
            pdb=" N   ILE B 123 "
            pdb=" C   ILE B 123 "
            pdb=" CB  ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.94e-01
  ... (remaining 1401 not shown)

  Planarity restraints: 1594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO B 236 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 138 "    0.010 2.00e-02 2.50e+03   1.90e-02 3.62e+00
        pdb=" C   LEU R 138 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LEU R 138 "    0.012 2.00e-02 2.50e+03
        pdb=" N   MET R 139 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 131 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   THR R 131 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   THR R 131 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU R 132 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1591 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 125
        2.66 -     3.22: 8325
        3.22 -     3.78: 14306
        3.78 -     4.34: 19806
        4.34 -     4.90: 32728
  Nonbonded interactions: 75290
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   SER N 112 "
            pdb=" NH2 ARG N 118 "
     model   vdw
     2.259 3.120
  ... (remaining 75285 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
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      :  0.004   0.047   9245  Z= 0.154
  Angle     :  0.551   6.898  12528  Z= 0.299
  Chirality :  0.042   0.145   1404
  Planarity :  0.004   0.053   1594
  Dihedral  : 14.120  86.912   3334
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.25), residues: 1130
  helix:  1.55 (0.25), residues: 428
  sheet: -0.19 (0.32), residues: 244
  loop : -0.81 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.017   0.002   TYR B  59 
 PHE   0.018   0.001   PHE B 234 
 TRP   0.013   0.002   TRP R 219 
 HIS   0.012   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9239)
  covalent geometry    : angle       0.54739 (12516)
  SS BOND              : bond        0.00271 (    6)
  SS BOND              : angle       2.20047 (   12)
  hydrogen bonds       : bond        0.13456 (  451)
  hydrogen bonds       : angle       6.34456 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.8197 (mt) cc_final: 0.7967 (mt)
REVERT: A  299 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7186 (mm-30)
REVERT: B  170 ASP cc_start: 0.7488 (t70) cc_final: 0.7106 (t70)
REVERT: B  175 GLN cc_start: 0.7673 (mm110) cc_final: 0.7331 (mp10)
REVERT: R   34 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6507 (tm-30)
REVERT: R  354 LYS cc_start: 0.6914 (mttp) cc_final: 0.6365 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.7558
  time to fit residues: 86.8847
Evaluate side-chains
  94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0020
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0870
   overall best weight:    0.3768

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 268 ASN
N  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.188648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.130350 restraints weight = 9037.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.01
r_work: 0.3153 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.0914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9245  Z= 0.112
  Angle     :  0.501   6.674  12528  Z= 0.269
  Chirality :  0.040   0.141   1404
  Planarity :  0.004   0.051   1594
  Dihedral  :  4.200  16.777   1247
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  8.32 %
    Favored  : 91.07 %
  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:  0.77 (0.26), residues: 1130
  helix:  2.19 (0.25), residues: 439
  sheet: -0.12 (0.32), residues: 250
  loop : -0.82 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.031   0.001   TYR R 130 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.011   0.001   TRP R 219 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9239)
  covalent geometry    : angle       0.50058 (12516)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       1.01387 (   12)
  hydrogen bonds       : bond        0.04118 (  451)
  hydrogen bonds       : angle       4.74306 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  296 LEU cc_start: 0.7670 (mt) cc_final: 0.7404 (mt)
REVERT: A  299 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: A  392 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7669 (mt-10)
REVERT: B  170 ASP cc_start: 0.7854 (t70) cc_final: 0.7408 (t70)
REVERT: B  175 GLN cc_start: 0.7681 (mm110) cc_final: 0.7315 (mp10)
REVERT: B  217 MET cc_start: 0.8167 (ptt) cc_final: 0.7661 (pp-130)
REVERT: N   35 ASN cc_start: 0.8039 (p0) cc_final: 0.7733 (p0)
REVERT: R   34 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6470 (tm-30)
REVERT: R  354 LYS cc_start: 0.6676 (mttp) cc_final: 0.6023 (ptmm)
REVERT: R  381 GLU cc_start: 0.7610 (tt0) cc_final: 0.7295 (pt0)
  outliers start: 6
  outliers final: 1
  residues processed: 113
  average time/residue: 0.6921
  time to fit residues: 82.9439
Evaluate side-chains
  103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0030
   chunk 50 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 387 HIS
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.186845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.128821 restraints weight = 8963.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.13
r_work: 0.3115 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9245  Z= 0.116
  Angle     :  0.482   6.368  12528  Z= 0.259
  Chirality :  0.040   0.144   1404
  Planarity :  0.003   0.049   1594
  Dihedral  :  4.034  15.895   1247
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.56 %
    Favored  : 87.72 %
  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:  0.86 (0.26), residues: 1130
  helix:  2.31 (0.25), residues: 442
  sheet: -0.03 (0.32), residues: 248
  loop : -0.88 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 137 
 TYR   0.026   0.001   TYR R 130 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.011   0.001   TRP R 219 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9239)
  covalent geometry    : angle       0.48114 (12516)
  SS BOND              : bond        0.00384 (    6)
  SS BOND              : angle       0.78612 (   12)
  hydrogen bonds       : bond        0.03989 (  451)
  hydrogen bonds       : angle       4.53212 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  296 LEU cc_start: 0.7868 (mt) cc_final: 0.7613 (mt)
REVERT: A  299 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7476 (mm-30)
REVERT: A  392 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7482 (mp0)
REVERT: B   76 ASP cc_start: 0.8748 (p0) cc_final: 0.8546 (p0)
REVERT: B  170 ASP cc_start: 0.7979 (t70) cc_final: 0.7560 (t70)
REVERT: B  175 GLN cc_start: 0.7665 (mm110) cc_final: 0.7300 (mp10)
REVERT: B  217 MET cc_start: 0.8171 (ptt) cc_final: 0.7690 (pp-130)
REVERT: N   35 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7984 (p0)
REVERT: N   53 GLN cc_start: 0.8209 (mp10) cc_final: 0.7938 (mp10)
REVERT: R   34 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6488 (tm-30)
REVERT: R  381 GLU cc_start: 0.7640 (tt0) cc_final: 0.7323 (pt0)
  outliers start: 17
  outliers final: 7
  residues processed: 122
  average time/residue: 0.6622
  time to fit residues: 85.8280
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain R residue  267 GLU
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  378 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 79 optimal weight:   50.0000
   chunk 107 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 268 ASN
R 155 HIS
R 379 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.183814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.123669 restraints weight = 8950.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.06
r_work: 0.3033 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   9245  Z= 0.238
  Angle     :  0.620  11.178  12528  Z= 0.327
  Chirality :  0.046   0.151   1404
  Planarity :  0.004   0.050   1594
  Dihedral  :  4.459  19.308   1247
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.88 %
    Favored  : 85.69 %
  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:  0.75 (0.26), residues: 1130
  helix:  2.13 (0.25), residues: 440
  sheet: -0.10 (0.32), residues: 249
  loop : -0.81 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 150 
 TYR   0.031   0.002   TYR R 130 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.016   0.002   TRP R 219 
 HIS   0.012   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 9239)
  covalent geometry    : angle       0.61051 (12516)
  SS BOND              : bond        0.00545 (    6)
  SS BOND              : angle       3.54684 (   12)
  hydrogen bonds       : bond        0.05023 (  451)
  hydrogen bonds       : angle       4.81387 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.7724 (mt) cc_final: 0.7456 (mt)
REVERT: A  299 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6849 (mm-30)
REVERT: A  392 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7438 (mp0)
REVERT: B  170 ASP cc_start: 0.8033 (t70) cc_final: 0.7498 (t70)
REVERT: B  175 GLN cc_start: 0.7842 (mm110) cc_final: 0.7473 (mp10)
REVERT: N   53 GLN cc_start: 0.8265 (mp10) cc_final: 0.7950 (mp10)
  outliers start: 24
  outliers final: 15
  residues processed: 118
  average time/residue: 0.5952
  time to fit residues: 74.8826
Evaluate side-chains
  112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   34 MET
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 18 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 61 optimal weight:    0.1980
   chunk 103 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 82 optimal weight:   20.0000
   chunk 95 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.184594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.126406 restraints weight = 8972.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.87
r_work: 0.3089 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9245  Z= 0.137
  Angle     :  0.516   6.384  12528  Z= 0.277
  Chirality :  0.041   0.145   1404
  Planarity :  0.004   0.051   1594
  Dihedral  :  4.221  17.248   1247
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.10 %
    Favored  : 83.96 %
  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:  0.85 (0.26), residues: 1130
  helix:  2.31 (0.25), residues: 439
  sheet: -0.16 (0.32), residues: 251
  loop : -0.78 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG N  72 
 TYR   0.022   0.001   TYR R 130 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.015   0.001   TRP R 219 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9239)
  covalent geometry    : angle       0.51390 (12516)
  SS BOND              : bond        0.00383 (    6)
  SS BOND              : angle       1.62377 (   12)
  hydrogen bonds       : bond        0.04139 (  451)
  hydrogen bonds       : angle       4.58656 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.7666 (mt) cc_final: 0.7412 (mt)
REVERT: A  299 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6869 (mm-30)
REVERT: A  392 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7295 (mp0)
REVERT: B  170 ASP cc_start: 0.7988 (t70) cc_final: 0.7474 (t70)
REVERT: B  175 GLN cc_start: 0.7744 (mm110) cc_final: 0.7363 (mp10)
REVERT: N   35 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7657 (p0)
REVERT: N   53 GLN cc_start: 0.8181 (mp10) cc_final: 0.7853 (mp10)
REVERT: R   35 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7133 (mp0)
REVERT: R  185 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7583 (p)
REVERT: R  267 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7473 (pt0)
REVERT: R  381 GLU cc_start: 0.7670 (tt0) cc_final: 0.7357 (pt0)
  outliers start: 29
  outliers final: 15
  residues processed: 115
  average time/residue: 0.6402
  time to fit residues: 78.3860
Evaluate side-chains
  116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  267 GLU
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  332 LEU
Chi-restraints excluded: chain R residue  378 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.0570
   chunk 45 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 79 optimal weight:   20.0000
   chunk 99 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.185578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.127011 restraints weight = 9038.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.91
r_work: 0.3110 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9245  Z= 0.113
  Angle     :  0.484   6.375  12528  Z= 0.260
  Chirality :  0.040   0.142   1404
  Planarity :  0.003   0.050   1594
  Dihedral  :  4.050  16.002   1247
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.21 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.95 (0.26), residues: 1130
  helix:  2.44 (0.25), residues: 439
  sheet: -0.13 (0.32), residues: 250
  loop : -0.76 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  72 
 TYR   0.021   0.001   TYR R 130 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.013   0.001   TRP R 219 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9239)
  covalent geometry    : angle       0.48235 (12516)
  SS BOND              : bond        0.00638 (    6)
  SS BOND              : angle       1.39753 (   12)
  hydrogen bonds       : bond        0.03805 (  451)
  hydrogen bonds       : angle       4.45483 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.7631 (mt) cc_final: 0.7378 (mt)
REVERT: A  299 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6752 (mm-30)
REVERT: A  392 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7283 (mp0)
REVERT: B  175 GLN cc_start: 0.7690 (mm110) cc_final: 0.7316 (mp10)
REVERT: N   35 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7366 (p0)
REVERT: N   53 GLN cc_start: 0.8082 (mp10) cc_final: 0.7786 (mp10)
REVERT: R   35 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7255 (mp0)
REVERT: R  185 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7555 (p)
REVERT: R  267 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7409 (pt0)
REVERT: R  381 GLU cc_start: 0.7626 (tt0) cc_final: 0.7328 (pt0)
  outliers start: 22
  outliers final: 10
  residues processed: 116
  average time/residue: 0.6456
  time to fit residues: 79.7703
Evaluate side-chains
  112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  267 GLU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

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 = 0.184713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.126295 restraints weight = 9053.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.88
r_work: 0.3099 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9245  Z= 0.135
  Angle     :  0.523  14.056  12528  Z= 0.279
  Chirality :  0.041   0.143   1404
  Planarity :  0.004   0.054   1594
  Dihedral  :  4.152  22.356   1247
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.92 %
    Favored  : 82.94 %
  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:  0.96 (0.26), residues: 1130
  helix:  2.45 (0.25), residues: 440
  sheet: -0.12 (0.33), residues: 250
  loop : -0.78 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  98 
 TYR   0.023   0.001   TYR R 130 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.013   0.001   TRP R 219 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9239)
  covalent geometry    : angle       0.50481 (12516)
  SS BOND              : bond        0.00385 (    6)
  SS BOND              : angle       4.46896 (   12)
  hydrogen bonds       : bond        0.04005 (  451)
  hydrogen bonds       : angle       4.47419 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.7687 (mt) cc_final: 0.7441 (mt)
REVERT: A  299 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6832 (mm-30)
REVERT: A  392 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7324 (mp0)
REVERT: B  170 ASP cc_start: 0.8015 (t70) cc_final: 0.7495 (t70)
REVERT: B  175 GLN cc_start: 0.7732 (mm110) cc_final: 0.7351 (mp10)
REVERT: N   35 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7260 (p0)
REVERT: N   53 GLN cc_start: 0.8086 (mp10) cc_final: 0.7804 (mp10)
REVERT: R   34 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6669 (tm-30)
REVERT: R   35 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: R  185 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7569 (p)
REVERT: R  267 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7467 (pt0)
REVERT: R  381 GLU cc_start: 0.7650 (tt0) cc_final: 0.7320 (pt0)
  outliers start: 21
  outliers final: 11
  residues processed: 120
  average time/residue: 0.6269
  time to fit residues: 80.1343
Evaluate side-chains
  115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  267 GLU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0670
   chunk 110 optimal weight:    3.9990
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.184272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.124525 restraints weight = 8994.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.98
r_work: 0.3081 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9245  Z= 0.122
  Angle     :  0.500  10.273  12528  Z= 0.268
  Chirality :  0.041   0.141   1404
  Planarity :  0.004   0.054   1594
  Dihedral  :  4.085  21.790   1247
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.63 %
    Favored  : 82.54 %
  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:  1.00 (0.26), residues: 1130
  helix:  2.51 (0.25), residues: 440
  sheet: -0.12 (0.33), residues: 250
  loop : -0.76 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG N  72 
 TYR   0.021   0.001   TYR R 130 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.013   0.001   TRP R 219 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9239)
  covalent geometry    : angle       0.49014 (12516)
  SS BOND              : bond        0.00318 (    6)
  SS BOND              : angle       3.21142 (   12)
  hydrogen bonds       : bond        0.03825 (  451)
  hydrogen bonds       : angle       4.41643 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.7710 (mt) cc_final: 0.7470 (mt)
REVERT: A  299 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6731 (mm-30)
REVERT: A  392 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7423 (mp0)
REVERT: B  170 ASP cc_start: 0.8093 (t70) cc_final: 0.7616 (t70)
REVERT: B  175 GLN cc_start: 0.7735 (mm110) cc_final: 0.7365 (mp10)
REVERT: N   35 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7381 (p0)
REVERT: N   53 GLN cc_start: 0.8018 (mp10) cc_final: 0.7738 (mp10)
REVERT: R   34 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6560 (tm-30)
REVERT: R   35 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: R  185 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7586 (p)
REVERT: R  267 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7426 (pt0)
REVERT: R  354 LYS cc_start: 0.6962 (mttt) cc_final: 0.6151 (ptmm)
REVERT: R  381 GLU cc_start: 0.7597 (tt0) cc_final: 0.7267 (pt0)
  outliers start: 18
  outliers final: 10
  residues processed: 113
  average time/residue: 0.5826
  time to fit residues: 69.9647
Evaluate side-chains
  114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  267 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 91 optimal weight:    0.4980
   chunk 90 optimal weight:    0.7980
   chunk 78 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.184847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.124632 restraints weight = 8979.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.06
r_work: 0.3110 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9245  Z= 0.114
  Angle     :  0.495   7.789  12528  Z= 0.265
  Chirality :  0.040   0.141   1404
  Planarity :  0.003   0.054   1594
  Dihedral  :  4.017  20.537   1247
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.74 %
    Favored  : 82.34 %
  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:  0.98 (0.26), residues: 1130
  helix:  2.45 (0.25), residues: 445
  sheet: -0.13 (0.33), residues: 251
  loop : -0.76 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG N  72 
 TYR   0.021   0.001   TYR R 130 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.013   0.001   TRP R 219 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9239)
  covalent geometry    : angle       0.48993 (12516)
  SS BOND              : bond        0.00335 (    6)
  SS BOND              : angle       2.43645 (   12)
  hydrogen bonds       : bond        0.03707 (  451)
  hydrogen bonds       : angle       4.36016 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.7782 (mt) cc_final: 0.7541 (mt)
REVERT: A  299 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6650 (mm-30)
REVERT: A  392 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7487 (mp0)
REVERT: B  175 GLN cc_start: 0.7656 (mm110) cc_final: 0.7291 (mp10)
REVERT: N   35 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7395 (p0)
REVERT: N   53 GLN cc_start: 0.8012 (mp10) cc_final: 0.7762 (mp10)
REVERT: N  108 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7751 (t80)
REVERT: R   34 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6393 (tm-30)
REVERT: R  185 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7563 (p)
REVERT: R  267 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7289 (pt0)
REVERT: R  354 LYS cc_start: 0.6959 (mttt) cc_final: 0.6161 (ptmm)
REVERT: R  381 GLU cc_start: 0.7648 (tt0) cc_final: 0.7370 (pt0)
  outliers start: 19
  outliers final: 10
  residues processed: 118
  average time/residue: 0.5267
  time to fit residues: 66.3463
Evaluate side-chains
  115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  267 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 78 optimal weight:   20.0000
   chunk 15 optimal weight:    0.7980
   chunk 83 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.186022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.127966 restraints weight = 8969.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.87
r_work: 0.3125 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9245  Z= 0.118
  Angle     :  0.504   7.628  12528  Z= 0.268
  Chirality :  0.041   0.142   1404
  Planarity :  0.003   0.054   1594
  Dihedral  :  4.023  20.230   1247
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.45 %
    Favored  : 82.03 %
  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:  0.99 (0.26), residues: 1130
  helix:  2.47 (0.25), residues: 445
  sheet: -0.13 (0.33), residues: 250
  loop : -0.77 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 388 
 TYR   0.021   0.001   TYR R 130 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.013   0.001   TRP R 219 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9239)
  covalent geometry    : angle       0.49970 (12516)
  SS BOND              : bond        0.00326 (    6)
  SS BOND              : angle       2.28121 (   12)
  hydrogen bonds       : bond        0.03723 (  451)
  hydrogen bonds       : angle       4.35148 ( 1302)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 LEU cc_start: 0.7762 (mt) cc_final: 0.7520 (mt)
REVERT: A  299 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6612 (mm-30)
REVERT: A  392 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7338 (mp0)
REVERT: B  175 GLN cc_start: 0.7565 (mm110) cc_final: 0.7179 (mp10)
REVERT: N   35 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7332 (p0)
REVERT: N   53 GLN cc_start: 0.7958 (mp10) cc_final: 0.7727 (mp10)
REVERT: N  108 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7679 (t80)
REVERT: R   34 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6413 (tm-30)
REVERT: R  185 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7496 (p)
REVERT: R  267 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7300 (pt0)
REVERT: R  354 LYS cc_start: 0.6934 (mttt) cc_final: 0.6145 (ptmm)
REVERT: R  381 GLU cc_start: 0.7626 (tt0) cc_final: 0.7405 (pt0)
  outliers start: 15
  outliers final: 11
  residues processed: 109
  average time/residue: 0.6398
  time to fit residues: 74.0260
Evaluate side-chains
  114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  267 GLU
Chi-restraints excluded: chain R residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0060
   chunk 65 optimal weight:    7.9990
   chunk 111 optimal weight:    0.1980
   chunk 97 optimal weight:    0.0020
   chunk 23 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.3604

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.189587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.132241 restraints weight = 8843.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.00
r_work: 0.3128 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9245  Z= 0.100
  Angle     :  0.481   7.668  12528  Z= 0.256
  Chirality :  0.040   0.139   1404
  Planarity :  0.003   0.054   1594
  Dihedral  :  3.884  19.680   1247
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.65 %
    Favored  : 81.83 %
  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:  1.07 (0.26), residues: 1130
  helix:  2.60 (0.25), residues: 440
  sheet: -0.11 (0.33), residues: 250
  loop : -0.74 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 388 
 TYR   0.019   0.001   TYR R 130 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.013   0.001   TRP R 219 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 9239)
  covalent geometry    : angle       0.47745 (12516)
  SS BOND              : bond        0.00314 (    6)
  SS BOND              : angle       1.95387 (   12)
  hydrogen bonds       : bond        0.03410 (  451)
  hydrogen bonds       : angle       4.24408 ( 1302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3918.36 seconds
wall clock time: 67 minutes 21.28 seconds (4041.28 seconds total)