Starting phenix.real_space_refine
on Fri Aug 22 19:57:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j12_61065/08_2025/9j12_61065.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j12_61065/08_2025/9j12_61065.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j12_61065/08_2025/9j12_61065.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j12_61065/08_2025/9j12_61065.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j12_61065/08_2025/9j12_61065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j12_61065/08_2025/9j12_61065.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.031
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      55      5.16       5
     C    4832      2.51       5
     N    1192      2.21       5
     O    1362      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7441
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 503, 3721
          Classifications: {'peptide': 503}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 486}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 3720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3720
          Classifications: {'peptide': 504}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 487}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 1.82, per 1000 atoms: 0.24
  Number of scatterers: 7441
  At special positions: 0
  Unit cell: (90.2, 99, 106.7, 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      55     16.00
     O    1362      8.00
     N    1192      7.00
     C    4832      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  72 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 232 " - pdb=" SG  CYS A 242 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B 101 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  77 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 242 " 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: 0.62
  Conformation dependent library (CDL) restraints added in 345.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1798

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 3 sheets defined
      66.0% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 24
      removed outlier: 4.012A  pdb=" N   SER A  10 " --> pdb=" O   THR A   6 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TRP A  11 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER A  12 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   MET A  14 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   LYS A  15 " --> pdb=" O   TRP A  11 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A  16 " --> pdb=" O   SER A  12 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   HIS A  17 " --> pdb=" O   ASP A  13 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A  21 " --> pdb=" O   HIS A  17 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LYS A  24 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 39 through 54
      removed outlier: 3.961A  pdb=" N   ARG A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   THR A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   MET A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 68
      removed outlier: 3.541A  pdb=" N   ASN A  61 " --> pdb=" O   ILE A  57 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ALA A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASP A  67 " --> pdb=" O   ASN A  63 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 78
    Processing helix  chain 'A' and resid 97 through 129
      removed outlier: 4.045A  pdb=" N   SER A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A 117 " --> pdb=" O   THR A 113 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   MET A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET A 124 " --> pdb=" O   GLY A 120 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASN A 129 " --> pdb=" O   GLY A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.586A  pdb=" N   ALA A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 180
      removed outlier: 3.714A  pdb=" N   GLY A 170 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ALA A 175 " --> pdb=" O   CYS A 171 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 187
      removed outlier: 3.856A  pdb=" N   ARG A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 209
      removed outlier: 4.040A  pdb=" N   ALA A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
      removed outlier: 3.566A  pdb=" N   ALA A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   VAL A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLY A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LYS A 268 " --> pdb=" O   PHE A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 3.800A  pdb=" N   ILE A 278 " --> pdb=" O   MET A 274 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ILE A 284 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 309
      removed outlier: 4.013A  pdb=" N   ASN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TYR A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASN A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 330
      removed outlier: 4.048A  pdb=" N   ARG A 330 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 327 through 330'
    Processing helix  chain 'A' and resid 331 through 360
      removed outlier: 4.510A  pdb=" N   TRP A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ALA A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU A 346 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LEU A 347 " --> pdb=" O   TYR A 343 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   GLY A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   VAL A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA A 357 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A 358 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 389
      removed outlier: 3.999A  pdb=" N   TYR A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LEU A 376 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   VAL A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASP A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 3.539A  pdb=" N   LYS A 404 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 3.510A  pdb=" N   MET A 424 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   PHE A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 430
      removed outlier: 3.667A  pdb=" N   VAL A 430 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 427 through 430'
    Processing helix  chain 'A' and resid 438 through 449
      removed outlier: 3.822A  pdb=" N   LEU A 442 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 443 " --> pdb=" O   GLY A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 451
      No H-bonds generated for 'chain 'A' and resid 450 through 451'
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.531A  pdb=" N   ILE A 456 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 478
      removed outlier: 4.358A  pdb=" N   THR A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ALA A 467 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   MET A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 480 through 495
      removed outlier: 3.950A  pdb=" N   ILE A 484 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A 486 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 505
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 4.322A  pdb=" N   SER B  12 " --> pdb=" O   CYS B   8 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   HIS B  17 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ASN B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 34 through 38
      removed outlier: 3.713A  pdb=" N   LYS B  37 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR B  38 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 34 through 38'
    Processing helix  chain 'B' and resid 40 through 55
      removed outlier: 4.027A  pdb=" N   LEU B  44 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ARG B  45 " --> pdb=" O   THR B  41 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   THR B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 66
    Processing helix  chain 'B' and resid 73 through 77
      removed outlier: 3.972A  pdb=" N   CYS B  77 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.928A  pdb=" N   CYS B  90 " --> pdb=" O   PRO B  86 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL B  91 " --> pdb=" O   GLY B  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 86 through 91'
    Processing helix  chain 'B' and resid 95 through 128
      removed outlier: 3.566A  pdb=" N   ASP B 108 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL B 110 " --> pdb=" O   LYS B 106 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   VAL B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET B 124 " --> pdb=" O   GLY B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 147
      removed outlier: 3.599A  pdb=" N   ILE B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 178
      removed outlier: 4.027A  pdb=" N   VAL B 166 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU B 167 " --> pdb=" O   MET B 163 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA B 175 " --> pdb=" O   CYS B 171 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER B 177 " --> pdb=" O   PHE B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 187
      removed outlier: 3.636A  pdb=" N   ARG B 187 " --> pdb=" O   GLY B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 208
      removed outlier: 3.985A  pdb=" N   ARG B 194 " --> pdb=" O   PRO B 190 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL B 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 211
      No H-bonds generated for 'chain 'B' and resid 209 through 211'
    Processing helix  chain 'B' and resid 249 through 267
      removed outlier: 3.632A  pdb=" N   TRP B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU B 254 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   MET B 267 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 285
      removed outlier: 4.374A  pdb=" N   VAL B 281 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 309
      removed outlier: 4.019A  pdb=" N   TYR B 307 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE B 308 " --> pdb=" O   ASN B 304 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR B 309 " --> pdb=" O   TYR B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 358
      removed outlier: 3.748A  pdb=" N   VAL B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ALA B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR B 349 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TYR B 354 " --> pdb=" O   THR B 350 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   THR B 355 " --> pdb=" O   GLY B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 385
      removed outlier: 3.994A  pdb=" N   TYR B 375 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU B 376 " --> pdb=" O   TYR B 372 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER B 382 " --> pdb=" O   ASP B 378 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL B 383 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 404
      removed outlier: 3.736A  pdb=" N   LEU B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 424
      removed outlier: 3.893A  pdb=" N   VAL B 414 " --> pdb=" O   GLY B 410 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER B 423 " --> pdb=" O   TYR B 419 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET B 424 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 430
      Proline residue:  B 428  - end of helix
      No H-bonds generated for 'chain 'B' and resid 425 through 430'
    Processing helix  chain 'B' and resid 437 through 450
      removed outlier: 4.163A  pdb=" N   SER B 441 " --> pdb=" O   ALA B 437 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   VAL B 447 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 474
      removed outlier: 3.654A  pdb=" N   ALA B 464 " --> pdb=" O   GLU B 460 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL B 465 " --> pdb=" O   THR B 461 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   THR B 466 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   MET B 474 " --> pdb=" O   THR B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 507
      removed outlier: 3.785A  pdb=" N   ILE B 484 " --> pdb=" O   ILE B 480 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA B 493 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   SER B 495 " --> pdb=" O   TYR B 491 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   TYR B 497 " --> pdb=" O   ALA B 493 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ASP B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   LEU B 501 " --> pdb=" O   TYR B 497 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLY B 502 " --> pdb=" O   ASP B 498 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 235
      removed outlier: 6.457A  pdb=" N   GLU A 234 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 134 through 135
      removed outlier: 4.568A  pdb=" N   ALA B 135 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA B 394 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 220

    335 hydrogen bonds defined for protein.
    996 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.99

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2300
        1.35 -     1.47: 1873
        1.47 -     1.59: 3326
        1.59 -     1.71: 1
        1.71 -     1.82: 93
  Bond restraints: 7593
  Sorted by residual:
  bond pdb=" CB  PRO A 296 "
       pdb=" CG  PRO A 296 "
    ideal  model  delta    sigma   weight residual
    1.492  1.649 -0.157 5.00e-02 4.00e+02 9.91e+00
  bond pdb=" N   PRO A 296 "
       pdb=" CA  PRO A 296 "
    ideal  model  delta    sigma   weight residual
    1.466  1.449  0.016 1.21e-02 6.83e+03 1.80e+00
  bond pdb=" CB  GLN B 191 "
       pdb=" CG  GLN B 191 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.51e+00
  bond pdb=" C   VAL A 344 "
       pdb=" O   VAL A 344 "
    ideal  model  delta    sigma   weight residual
    1.231  1.244 -0.012 1.02e-02 9.61e+03 1.48e+00
  bond pdb=" CA  ASP A 455 "
       pdb=" CB  ASP A 455 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.26e+00
  ... (remaining 7588 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 10180
        2.85 -     5.71: 104
        5.71 -     8.56: 30
        8.56 -    11.42: 8
       11.42 -    14.27: 1
  Bond angle restraints: 10323
  Sorted by residual:
  angle pdb=" CA  PRO A 296 "
        pdb=" N   PRO A 296 "
        pdb=" CD  PRO A 296 "
      ideal   model   delta    sigma   weight residual
     112.00   97.73   14.27 1.40e+00 5.10e-01 1.04e+02
  angle pdb=" N   VAL B 176 "
        pdb=" CA  VAL B 176 "
        pdb=" C   VAL B 176 "
      ideal   model   delta    sigma   weight residual
     113.71  107.02    6.69 9.50e-01 1.11e+00 4.96e+01
  angle pdb=" C   LYS A  37 "
        pdb=" CA  LYS A  37 "
        pdb=" CB  LYS A  37 "
      ideal   model   delta    sigma   weight residual
     110.16  119.58   -9.42 1.44e+00 4.82e-01 4.28e+01
  angle pdb=" C   PRO A 296 "
        pdb=" CA  PRO A 296 "
        pdb=" CB  PRO A 296 "
      ideal   model   delta    sigma   weight residual
     111.12  103.30    7.82 1.29e+00 6.01e-01 3.68e+01
  angle pdb=" N   THR A  38 "
        pdb=" CA  THR A  38 "
        pdb=" CB  THR A  38 "
      ideal   model   delta    sigma   weight residual
     110.99  119.73   -8.74 1.77e+00 3.19e-01 2.44e+01
  ... (remaining 10318 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.11: 3996
       18.11 -    36.22: 338
       36.22 -    54.32: 83
       54.32 -    72.43: 4
       72.43 -    90.54: 4
  Dihedral angle restraints: 4425
    sinusoidal: 1590
      harmonic: 2835
  Sorted by residual:
  dihedral pdb=" CA  ARG A  36 "
           pdb=" C   ARG A  36 "
           pdb=" N   LYS A  37 "
           pdb=" CA  LYS A  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.62  -27.38     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CB  CYS B  77 "
           pdb=" SG  CYS B  77 "
           pdb=" SG  CYS B  90 "
           pdb=" CB  CYS B  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.62  -39.62     1      1.00e+01 1.00e-02 2.21e+01
  dihedral pdb=" CB  CYS A  77 "
           pdb=" SG  CYS A  77 "
           pdb=" SG  CYS A  90 "
           pdb=" CB  CYS A  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.47   39.53     1      1.00e+01 1.00e-02 2.20e+01
  ... (remaining 4422 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 790
       0.037 -    0.074: 354
       0.074 -    0.111: 84
       0.111 -    0.148: 17
       0.148 -    0.185: 5
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CB  VAL A 105 "
            pdb=" CA  VAL A 105 "
            pdb=" CG1 VAL A 105 "
            pdb=" CG2 VAL A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  HIS A 297 "
            pdb=" N   HIS A 297 "
            pdb=" C   HIS A 297 "
            pdb=" CB  HIS A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.87e-01
  chirality pdb=" CA  MET B  14 "
            pdb=" N   MET B  14 "
            pdb=" C   MET B  14 "
            pdb=" CB  MET B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.62e-01
  ... (remaining 1247 not shown)

  Planarity restraints: 1270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 295 "    0.124 5.00e-02 4.00e+02   1.76e-01 4.94e+01
        pdb=" N   PRO A 296 "   -0.303 5.00e-02 4.00e+02
        pdb=" CA  PRO A 296 "    0.094 5.00e-02 4.00e+02
        pdb=" CD  PRO A 296 "    0.085 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 130 "   -0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO A 131 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 131 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 131 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  17 "   -0.013 2.00e-02 2.50e+03   1.24e-02 2.32e+00
        pdb=" CG  HIS B  17 "    0.026 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  17 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1267 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 157
        2.69 -     3.24: 7845
        3.24 -     3.80: 11186
        3.80 -     4.35: 14141
        4.35 -     4.90: 23041
  Nonbonded interactions: 56370
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  61 "
            pdb=" ND2 ASN B 141 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" OD2 ASP B 108 "
            pdb=" OG1 THR B 320 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OG1 THR B 192 "
            pdb=" OE1 GLU B 463 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LEU A 346 "
            pdb=" OG1 THR A 350 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ASP A 345 "
            pdb=" OG1 THR A 349 "
     model   vdw
     2.277 3.040
  ... (remaining 56365 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 504 or (resid 505 through 507 and (name N or nam \ 
e CA or name C or name O or name CB ))))
  selection = (chain 'B' and ((resid 5 through 9 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 10 through 507))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.410
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
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      :  0.003   0.157   7599  Z= 0.154
  Angle     :  0.858  14.270  10335  Z= 0.489
  Chirality :  0.043   0.185   1250
  Planarity :  0.006   0.176   1270
  Dihedral  : 14.032  90.541   2609
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.70 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.25), residues: 1003
  helix: -0.70 (0.21), residues: 555
  sheet:  None (None), residues: 0
  loop : -2.78 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 182 
 TYR   0.014   0.001   TYR A  56 
 PHE   0.026   0.001   PHE A 173 
 TRP   0.026   0.001   TRP A 335 
 HIS   0.011   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7593)
  covalent geometry    : angle       0.85732 (10323)
  SS BOND              : bond        0.00337 (    6)
  SS BOND              : angle       1.55614 (   12)
  hydrogen bonds       : bond        0.21812 (  335)
  hydrogen bonds       : angle       6.55178 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  335 TRP cc_start: 0.7218 (m-90) cc_final: 0.6340 (m-90)
REVERT: A  356 MET cc_start: 0.7776 (mmm) cc_final: 0.7432 (mmp)
REVERT: A  375 TYR cc_start: 0.8192 (m-10) cc_final: 0.7977 (m-10)
REVERT: A  418 LEU cc_start: 0.8458 (mm) cc_final: 0.8104 (tt)
REVERT: A  444 MET cc_start: 0.8693 (tpp) cc_final: 0.8133 (tpp)
REVERT: B  168 LEU cc_start: 0.8323 (mt) cc_final: 0.7998 (mt)
REVERT: B  169 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8705 (tm-30)
REVERT: B  267 MET cc_start: 0.8497 (mmm) cc_final: 0.8083 (mmm)
REVERT: B  456 ILE cc_start: 0.8911 (mp) cc_final: 0.8618 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0669
  time to fit residues: 17.3942
Evaluate side-chains
  161 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.152115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.119699 restraints weight = 15743.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.123301 restraints weight = 8565.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.125608 restraints weight = 5735.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.127115 restraints weight = 4435.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.127788 restraints weight = 3777.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7599  Z= 0.135
  Angle     :  0.650   9.151  10335  Z= 0.323
  Chirality :  0.042   0.150   1250
  Planarity :  0.005   0.096   1270
  Dihedral  :  4.733  27.251   1061
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 25.22 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.26), residues: 1003
  helix: -0.26 (0.22), residues: 570
  sheet: -3.14 (1.56), residues: 10
  loop : -2.75 (0.27), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  29 
 TYR   0.011   0.001   TYR B 146 
 PHE   0.014   0.001   PHE B  40 
 TRP   0.024   0.001   TRP A 335 
 HIS   0.011   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7593)
  covalent geometry    : angle       0.64908 (10323)
  SS BOND              : bond        0.00196 (    6)
  SS BOND              : angle       1.14551 (   12)
  hydrogen bonds       : bond        0.04402 (  335)
  hydrogen bonds       : angle       4.52689 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 177
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7776 (tp30) cc_final: 0.7108 (tp30)
REVERT: A  173 PHE cc_start: 0.8594 (m-10) cc_final: 0.8100 (m-10)
REVERT: A  356 MET cc_start: 0.8054 (mmm) cc_final: 0.7673 (mmp)
REVERT: A  444 MET cc_start: 0.8862 (tpp) cc_final: 0.8310 (tpp)
REVERT: B  163 MET cc_start: 0.7468 (mmm) cc_final: 0.7205 (mmm)
REVERT: B  203 MET cc_start: 0.8830 (tpp) cc_final: 0.8543 (tpp)
REVERT: B  286 TRP cc_start: 0.8737 (OUTLIER) cc_final: 0.8179 (m-10)
REVERT: B  478 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7746 (m-80)
  outliers start: 30
  outliers final: 17
  residues processed: 191
  average time/residue: 0.0578
  time to fit residues: 16.1278
Evaluate side-chains
  177 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  416 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0470
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.9282

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.149960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.117714 restraints weight = 15658.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.121222 restraints weight = 8518.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.123528 restraints weight = 5737.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.125007 restraints weight = 4457.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.125824 restraints weight = 3810.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7599  Z= 0.123
  Angle     :  0.641   7.955  10335  Z= 0.312
  Chirality :  0.041   0.143   1250
  Planarity :  0.004   0.069   1270
  Dihedral  :  4.613  23.934   1061
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 26.74 %
    Favored  : 68.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.26), residues: 1003
  helix: -0.12 (0.22), residues: 582
  sheet: -2.98 (1.68), residues: 10
  loop : -2.74 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 182 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.010   0.001   PHE B 314 
 TRP   0.017   0.001   TRP A 335 
 HIS   0.009   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7593)
  covalent geometry    : angle       0.64042 (10323)
  SS BOND              : bond        0.00612 (    6)
  SS BOND              : angle       0.94270 (   12)
  hydrogen bonds       : bond        0.03615 (  335)
  hydrogen bonds       : angle       4.17385 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 170
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7940 (tp30) cc_final: 0.7625 (tp30)
REVERT: A  356 MET cc_start: 0.8276 (mmm) cc_final: 0.7976 (mmp)
REVERT: A  444 MET cc_start: 0.8879 (tpp) cc_final: 0.8287 (tpp)
REVERT: B   14 MET cc_start: 0.8351 (mpp) cc_final: 0.7900 (mpp)
REVERT: B  163 MET cc_start: 0.7405 (mmm) cc_final: 0.7105 (mmm)
REVERT: B  229 LEU cc_start: 0.8615 (pt) cc_final: 0.8313 (tt)
REVERT: B  286 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.7891 (m-10)
REVERT: B  456 ILE cc_start: 0.9011 (mp) cc_final: 0.8746 (mm)
REVERT: B  478 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7785 (m-80)
  outliers start: 39
  outliers final: 24
  residues processed: 196
  average time/residue: 0.0582
  time to fit residues: 16.8500
Evaluate side-chains
  187 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 161
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  478 TYR
Chi-restraints excluded: chain B residue  497 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 78 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.149803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.116891 restraints weight = 15951.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.120426 restraints weight = 8706.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.122715 restraints weight = 5883.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.124031 restraints weight = 4591.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.125070 restraints weight = 3974.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7599  Z= 0.116
  Angle     :  0.638  10.365  10335  Z= 0.305
  Chirality :  0.041   0.147   1250
  Planarity :  0.004   0.057   1270
  Dihedral  :  4.488  20.433   1061
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.25 %
    Favored  : 67.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.26), residues: 1003
  helix:  0.12 (0.22), residues: 584
  sheet: -2.83 (1.78), residues: 10
  loop : -2.66 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 182 
 TYR   0.019   0.001   TYR A 375 
 PHE   0.014   0.001   PHE A 173 
 TRP   0.012   0.001   TRP A 335 
 HIS   0.007   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7593)
  covalent geometry    : angle       0.63794 (10323)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       0.91494 (   12)
  hydrogen bonds       : bond        0.03307 (  335)
  hydrogen bonds       : angle       4.06559 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 174
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8305 (mmm) cc_final: 0.8041 (mmp)
REVERT: A  358 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8118 (mp0)
REVERT: A  444 MET cc_start: 0.8868 (tpp) cc_final: 0.8371 (tpp)
REVERT: B  163 MET cc_start: 0.7401 (mmm) cc_final: 0.7159 (mmm)
REVERT: B  229 LEU cc_start: 0.8625 (pt) cc_final: 0.8382 (tt)
REVERT: B  267 MET cc_start: 0.8707 (mmm) cc_final: 0.8387 (mmm)
REVERT: B  286 TRP cc_start: 0.8731 (OUTLIER) cc_final: 0.7875 (m-10)
REVERT: B  343 TYR cc_start: 0.8136 (t80) cc_final: 0.7860 (t80)
REVERT: B  424 MET cc_start: 0.8765 (ppp) cc_final: 0.8524 (ppp)
REVERT: B  478 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.7894 (m-80)
  outliers start: 39
  outliers final: 28
  residues processed: 197
  average time/residue: 0.0622
  time to fit residues: 17.6968
Evaluate side-chains
  184 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 7 optimal weight:   30.0000
   chunk 80 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0050
   chunk 70 optimal weight:    0.3980
   chunk 92 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.151356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.119205 restraints weight = 15896.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.122835 restraints weight = 8627.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.125174 restraints weight = 5762.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.126746 restraints weight = 4442.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.127716 restraints weight = 3763.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7599  Z= 0.102
  Angle     :  0.626   9.264  10335  Z= 0.296
  Chirality :  0.041   0.134   1250
  Planarity :  0.004   0.050   1270
  Dihedral  :  4.313  20.644   1061
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 27.63 %
    Favored  : 67.55 %
  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 aren not related in a simple way.
  whole: -1.36 (0.26), residues: 1003
  helix:  0.24 (0.22), residues: 589
  sheet:  None (None), residues: 0
  loop : -2.66 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 182 
 TYR   0.014   0.001   TYR B 143 
 PHE   0.014   0.001   PHE A 173 
 TRP   0.010   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7593)
  covalent geometry    : angle       0.62423 (10323)
  SS BOND              : bond        0.00271 (    6)
  SS BOND              : angle       1.39181 (   12)
  hydrogen bonds       : bond        0.03116 (  335)
  hydrogen bonds       : angle       3.87845 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 178
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.4792 (t80)
REVERT: A  159 TYR cc_start: 0.8190 (t80) cc_final: 0.7908 (t80)
REVERT: A  211 GLN cc_start: 0.7629 (mp10) cc_final: 0.7330 (mp10)
REVERT: A  335 TRP cc_start: 0.7678 (m-10) cc_final: 0.7026 (m-90)
REVERT: A  358 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8150 (mp0)
REVERT: A  444 MET cc_start: 0.8733 (tpp) cc_final: 0.8242 (tpp)
REVERT: B  163 MET cc_start: 0.7353 (mmm) cc_final: 0.7059 (mmm)
REVERT: B  179 LEU cc_start: 0.7928 (pt) cc_final: 0.6758 (tp)
REVERT: B  267 MET cc_start: 0.8774 (mmm) cc_final: 0.8509 (mmm)
REVERT: B  286 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.7967 (m-10)
REVERT: B  424 MET cc_start: 0.8801 (ppp) cc_final: 0.8577 (ppp)
REVERT: B  462 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8782 (tptm)
REVERT: B  478 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8000 (m-80)
  outliers start: 38
  outliers final: 23
  residues processed: 200
  average time/residue: 0.0612
  time to fit residues: 17.9983
Evaluate side-chains
  190 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  441 SER
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  462 LYS
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0050
   chunk 90 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.1800

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

Flipped N/Q/H residues before XYZ refinement:
B 315 HIS

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 = 0.146709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.113653 restraints weight = 15905.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.117071 restraints weight = 8735.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.119294 restraints weight = 5927.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.120736 restraints weight = 4630.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.121638 restraints weight = 3972.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7599  Z= 0.136
  Angle     :  0.677   9.232  10335  Z= 0.322
  Chirality :  0.043   0.274   1250
  Planarity :  0.004   0.047   1270
  Dihedral  :  4.479  20.601   1061
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 26.62 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.26), residues: 1003
  helix:  0.31 (0.22), residues: 593
  sheet: -2.99 (1.80), residues: 10
  loop : -2.62 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 182 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.023   0.001   PHE A 173 
 TRP   0.007   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7593)
  covalent geometry    : angle       0.67483 (10323)
  SS BOND              : bond        0.00243 (    6)
  SS BOND              : angle       1.61571 (   12)
  hydrogen bonds       : bond        0.03451 (  335)
  hydrogen bonds       : angle       4.03686 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 168
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 TYR cc_start: 0.8226 (t80) cc_final: 0.7920 (t80)
REVERT: A  335 TRP cc_start: 0.7725 (m-10) cc_final: 0.7104 (m-90)
REVERT: A  356 MET cc_start: 0.8567 (mmp) cc_final: 0.8209 (mmm)
REVERT: A  358 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8053 (mp0)
REVERT: A  444 MET cc_start: 0.8875 (tpp) cc_final: 0.8534 (tpp)
REVERT: B  141 ASN cc_start: 0.8681 (m110) cc_final: 0.8379 (m110)
REVERT: B  251 THR cc_start: 0.9091 (p) cc_final: 0.8630 (t)
REVERT: B  267 MET cc_start: 0.8834 (mmm) cc_final: 0.8588 (mmm)
REVERT: B  286 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.8477 (m-10)
REVERT: B  343 TYR cc_start: 0.8130 (t80) cc_final: 0.7754 (t80)
  outliers start: 48
  outliers final: 34
  residues processed: 197
  average time/residue: 0.0626
  time to fit residues: 17.8923
Evaluate side-chains
  195 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 160
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  471 ILE
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.147941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.114880 restraints weight = 15938.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.118403 restraints weight = 8688.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.120654 restraints weight = 5837.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.122120 restraints weight = 4537.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.123036 restraints weight = 3884.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7599  Z= 0.119
  Angle     :  0.679  11.029  10335  Z= 0.319
  Chirality :  0.043   0.238   1250
  Planarity :  0.004   0.044   1270
  Dihedral  :  4.485  20.081   1061
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 28.39 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.26), residues: 1003
  helix:  0.38 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.63 (0.27), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 182 
 TYR   0.017   0.001   TYR B 159 
 PHE   0.020   0.001   PHE A 173 
 TRP   0.009   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7593)
  covalent geometry    : angle       0.67888 (10323)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       0.82307 (   12)
  hydrogen bonds       : bond        0.03196 (  335)
  hydrogen bonds       : angle       3.92078 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 168
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.8838 (m) cc_final: 0.8522 (p)
REVERT: A   98 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.4792 (t80)
REVERT: A  159 TYR cc_start: 0.8272 (t80) cc_final: 0.8000 (t80)
REVERT: A  318 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7809 (tp-100)
REVERT: A  335 TRP cc_start: 0.7726 (m-10) cc_final: 0.7153 (m-90)
REVERT: A  341 LEU cc_start: 0.8234 (pp) cc_final: 0.7915 (pp)
REVERT: A  345 ASP cc_start: 0.7310 (m-30) cc_final: 0.6953 (m-30)
REVERT: A  356 MET cc_start: 0.8566 (mmp) cc_final: 0.8149 (mmm)
REVERT: A  358 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8089 (mp0)
REVERT: A  444 MET cc_start: 0.8808 (tpp) cc_final: 0.8334 (tpp)
REVERT: B  141 ASN cc_start: 0.8510 (m110) cc_final: 0.8232 (m110)
REVERT: B  251 THR cc_start: 0.9026 (p) cc_final: 0.8550 (t)
REVERT: B  267 MET cc_start: 0.8815 (mmm) cc_final: 0.8575 (mmm)
REVERT: B  286 TRP cc_start: 0.8739 (OUTLIER) cc_final: 0.8475 (m-10)
REVERT: B  343 TYR cc_start: 0.8074 (t80) cc_final: 0.7636 (t80)
  outliers start: 34
  outliers final: 26
  residues processed: 189
  average time/residue: 0.0600
  time to fit residues: 16.2307
Evaluate side-chains
  188 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  132 PHE
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  286 TRP
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 71 optimal weight:    0.2980
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 82 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 211 GLN
B 297 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.146097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.112857 restraints weight = 16054.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.116286 restraints weight = 8703.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.118559 restraints weight = 5866.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.119813 restraints weight = 4563.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.120818 restraints weight = 3958.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7599  Z= 0.132
  Angle     :  0.697  10.434  10335  Z= 0.329
  Chirality :  0.043   0.227   1250
  Planarity :  0.004   0.051   1270
  Dihedral  :  4.557  20.362   1061
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 29.40 %
    Favored  : 66.54 %
  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 aren not related in a simple way.
  whole: -1.14 (0.26), residues: 1003
  helix:  0.44 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.66 (0.28), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 182 
 TYR   0.013   0.001   TYR A 343 
 PHE   0.019   0.001   PHE A 173 
 TRP   0.007   0.001   TRP B  11 
 HIS   0.007   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7593)
  covalent geometry    : angle       0.69492 (10323)
  SS BOND              : bond        0.00326 (    6)
  SS BOND              : angle       1.80972 (   12)
  hydrogen bonds       : bond        0.03325 (  335)
  hydrogen bonds       : angle       3.96326 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.4858 (t80)
REVERT: A  159 TYR cc_start: 0.8360 (t80) cc_final: 0.8074 (t80)
REVERT: A  213 ASN cc_start: 0.7463 (t0) cc_final: 0.6927 (t0)
REVERT: A  318 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7765 (tp-100)
REVERT: A  335 TRP cc_start: 0.7736 (m-10) cc_final: 0.7159 (m-90)
REVERT: A  341 LEU cc_start: 0.8298 (pp) cc_final: 0.7960 (pp)
REVERT: A  345 ASP cc_start: 0.7337 (m-30) cc_final: 0.6900 (m-30)
REVERT: A  356 MET cc_start: 0.8659 (mmp) cc_final: 0.8113 (mmm)
REVERT: A  358 GLU cc_start: 0.8568 (tm-30) cc_final: 0.7912 (mp0)
REVERT: A  359 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8623 (tp)
REVERT: A  444 MET cc_start: 0.8849 (tpp) cc_final: 0.8410 (tpp)
REVERT: B  163 MET cc_start: 0.6860 (mmm) cc_final: 0.6633 (mmt)
REVERT: B  251 THR cc_start: 0.9071 (p) cc_final: 0.8606 (t)
REVERT: B  267 MET cc_start: 0.8741 (mmm) cc_final: 0.8496 (mmm)
REVERT: B  343 TYR cc_start: 0.8134 (t80) cc_final: 0.7657 (t80)
  outliers start: 32
  outliers final: 28
  residues processed: 184
  average time/residue: 0.0563
  time to fit residues: 15.1570
Evaluate side-chains
  198 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue   94 SER
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0870
   chunk 78 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
A 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.145880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.112889 restraints weight = 15714.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.116263 restraints weight = 8539.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.118528 restraints weight = 5769.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.119921 restraints weight = 4488.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.120545 restraints weight = 3858.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7599  Z= 0.124
  Angle     :  0.689  11.296  10335  Z= 0.327
  Chirality :  0.042   0.209   1250
  Planarity :  0.004   0.058   1270
  Dihedral  :  4.516  22.065   1061
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 29.53 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.27), residues: 1003
  helix:  0.49 (0.22), residues: 597
  sheet:  None (None), residues: 0
  loop : -2.65 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 182 
 TYR   0.013   0.001   TYR A 343 
 PHE   0.024   0.001   PHE B 132 
 TRP   0.007   0.001   TRP B  11 
 HIS   0.010   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7593)
  covalent geometry    : angle       0.68747 (10323)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       1.56902 (   12)
  hydrogen bonds       : bond        0.03252 (  335)
  hydrogen bonds       : angle       3.91238 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.9400 (ptmt) cc_final: 0.9194 (ptmt)
REVERT: A   73 SER cc_start: 0.9097 (m) cc_final: 0.8727 (p)
REVERT: A   98 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.4843 (t80)
REVERT: A  159 TYR cc_start: 0.8467 (t80) cc_final: 0.8211 (t80)
REVERT: A  181 LEU cc_start: 0.8881 (pp) cc_final: 0.8453 (mt)
REVERT: A  213 ASN cc_start: 0.7474 (t0) cc_final: 0.7040 (t0)
REVERT: A  318 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7711 (tp-100)
REVERT: A  335 TRP cc_start: 0.7731 (m-10) cc_final: 0.7158 (m-90)
REVERT: A  341 LEU cc_start: 0.8277 (pp) cc_final: 0.7848 (pp)
REVERT: A  345 ASP cc_start: 0.7365 (m-30) cc_final: 0.6961 (m-30)
REVERT: A  356 MET cc_start: 0.8652 (mmp) cc_final: 0.8113 (mmm)
REVERT: A  358 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7905 (mp0)
REVERT: A  359 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8620 (tp)
REVERT: A  444 MET cc_start: 0.8803 (tpp) cc_final: 0.8316 (tpp)
REVERT: B  124 MET cc_start: 0.8179 (tpp) cc_final: 0.7655 (tpt)
REVERT: B  251 THR cc_start: 0.9059 (p) cc_final: 0.8588 (t)
REVERT: B  267 MET cc_start: 0.8648 (mmm) cc_final: 0.8394 (mmm)
  outliers start: 34
  outliers final: 29
  residues processed: 189
  average time/residue: 0.0561
  time to fit residues: 15.7674
Evaluate side-chains
  198 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0010
   chunk 41 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.147340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.114422 restraints weight = 15836.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.117873 restraints weight = 8569.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.120163 restraints weight = 5750.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.121440 restraints weight = 4470.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.122438 restraints weight = 3866.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7599  Z= 0.114
  Angle     :  0.692  11.464  10335  Z= 0.324
  Chirality :  0.042   0.194   1250
  Planarity :  0.004   0.054   1270
  Dihedral  :  4.434  25.064   1061
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 29.66 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.27), residues: 1003
  helix:  0.56 (0.22), residues: 597
  sheet:  None (None), residues: 0
  loop : -2.61 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 182 
 TYR   0.012   0.001   TYR A 343 
 PHE   0.024   0.001   PHE B 132 
 TRP   0.007   0.001   TRP B  11 
 HIS   0.011   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7593)
  covalent geometry    : angle       0.69104 (10323)
  SS BOND              : bond        0.00185 (    6)
  SS BOND              : angle       1.31239 (   12)
  hydrogen bonds       : bond        0.03118 (  335)
  hydrogen bonds       : angle       3.81328 (  996)

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 176
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.9398 (ptmt) cc_final: 0.9197 (ptmt)
REVERT: A   73 SER cc_start: 0.9121 (m) cc_final: 0.8471 (p)
REVERT: A   98 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.4858 (t80)
REVERT: A  159 TYR cc_start: 0.8513 (t80) cc_final: 0.8283 (t80)
REVERT: A  181 LEU cc_start: 0.8892 (pp) cc_final: 0.8474 (mt)
REVERT: A  318 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7757 (tp-100)
REVERT: A  335 TRP cc_start: 0.7712 (m-10) cc_final: 0.7154 (m-90)
REVERT: A  341 LEU cc_start: 0.8081 (pp) cc_final: 0.7704 (pp)
REVERT: A  345 ASP cc_start: 0.7360 (m-30) cc_final: 0.6997 (m-30)
REVERT: A  356 MET cc_start: 0.8607 (mmp) cc_final: 0.8122 (mmm)
REVERT: A  358 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7918 (mp0)
REVERT: A  444 MET cc_start: 0.8812 (tpp) cc_final: 0.8521 (tpp)
REVERT: B   36 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7319 (mtt180)
REVERT: B  251 THR cc_start: 0.9034 (p) cc_final: 0.8557 (t)
REVERT: B  267 MET cc_start: 0.8641 (mmm) cc_final: 0.8375 (mmm)
REVERT: B  343 TYR cc_start: 0.8041 (t80) cc_final: 0.7716 (t80)
  outliers start: 31
  outliers final: 27
  residues processed: 192
  average time/residue: 0.0583
  time to fit residues: 16.6183
Evaluate side-chains
  200 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 172
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   77 CYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  256 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  478 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0770
   chunk 28 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.146960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.114033 restraints weight = 15688.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.117464 restraints weight = 8552.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.119720 restraints weight = 5754.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.120918 restraints weight = 4481.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.121887 restraints weight = 3892.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7599  Z= 0.118
  Angle     :  0.705  11.488  10335  Z= 0.330
  Chirality :  0.042   0.186   1250
  Planarity :  0.004   0.048   1270
  Dihedral  :  4.410  25.432   1061
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 31.31 %
    Favored  : 65.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.26), residues: 1003
  helix:  0.55 (0.22), residues: 597
  sheet:  None (None), residues: 0
  loop : -2.64 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 182 
 TYR   0.013   0.001   TYR B 146 
 PHE   0.027   0.001   PHE B 132 
 TRP   0.008   0.001   TRP B  11 
 HIS   0.009   0.001   HIS B  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7593)
  covalent geometry    : angle       0.70393 (10323)
  SS BOND              : bond        0.00185 (    6)
  SS BOND              : angle       1.33726 (   12)
  hydrogen bonds       : bond        0.03179 (  335)
  hydrogen bonds       : angle       3.84368 (  996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1266.04 seconds
wall clock time: 22 minutes 31.38 seconds (1351.38 seconds total)