Starting phenix.real_space_refine
on Fri Jun  6 09:05:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j12_61065/06_2025/9j12_61065.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j12_61065/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j12_61065/06_2025/9j12_61065.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j12_61065/06_2025/9j12_61065.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j12_61065/06_2025/9j12_61065.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j12_61065/06_2025/9j12_61065.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 4.63, per 1000 atoms: 0.62
  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: 2.04
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.74
  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: 1.87

  Time building geometry restraints manager: 2.41 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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.750
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.120
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.026   0.001   TRP A 335 
 HIS   0.011   0.001   HIS B  17 
 PHE   0.026   0.001   PHE A 173 
 TYR   0.014   0.001   TYR A  56 
 ARG   0.006   0.001   ARG B 182 

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

*********************** 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  : 0.897 
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: 0.8103 (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: 0.8617 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1795
  time to fit residues: 45.9561
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  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0270
   chunk 58 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   overall best weight:    0.7238

-------------------------------------------------------------------------------
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 = 0.4091 r_free = 0.4091 target = 0.153415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.121244 restraints weight = 15402.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.124860 restraints weight = 8417.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.127172 restraints weight = 5646.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1904

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= 0.125
  Angle     :  0.639   9.167  10335  Z= 0.316
  Chirality :  0.042   0.145   1250
  Planarity :  0.005   0.096   1270
  Dihedral  :  4.699  27.107   1061
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.22 %
    Favored  : 71.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.26), residues: 1003
  helix: -0.31 (0.22), residues: 574
  sheet: -3.15 (1.55), residues: 10
  loop : -2.74 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 335 
 HIS   0.009   0.001   HIS B  17 
 PHE   0.015   0.001   PHE B  40 
 TYR   0.009   0.001   TYR A 305 
 ARG   0.006   0.001   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04183 (  335)
  hydrogen bonds       : angle       4.47040 (  996)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       1.09993 (   12)
  covalent geometry    : bond        0.00278 ( 7593)
  covalent geometry    : angle       0.63845 (10323)

*********************** 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
  203 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7780 (tp30) cc_final: 0.7007 (tp30)
REVERT: A  173 PHE cc_start: 0.8543 (m-10) cc_final: 0.8030 (m-10)
REVERT: A  356 MET cc_start: 0.7969 (mmm) cc_final: 0.7570 (mmp)
REVERT: A  421 LEU cc_start: 0.8788 (tp) cc_final: 0.8586 (tp)
REVERT: A  444 MET cc_start: 0.8866 (tpp) cc_final: 0.8295 (tpp)
REVERT: B  163 MET cc_start: 0.7463 (mmm) cc_final: 0.7185 (mmm)
REVERT: B  286 TRP cc_start: 0.8737 (OUTLIER) cc_final: 0.8183 (m-10)
  outliers start: 26
  outliers final: 15
  residues processed: 188
  average time/residue: 0.1571
  time to fit residues: 42.0118
Evaluate side-chains
  175 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
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  181 LEU
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 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  416 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 62 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0370
   chunk 81 optimal weight:    6.9990
   chunk 8 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    8.9990
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
A 160 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.154351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.122163 restraints weight = 15858.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.125801 restraints weight = 8614.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.128179 restraints weight = 5759.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7599  Z= 0.107
  Angle     :  0.627  10.373  10335  Z= 0.302
  Chirality :  0.040   0.146   1250
  Planarity :  0.004   0.066   1270
  Dihedral  :  4.449  23.803   1061
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 28.52 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.26), residues: 1003
  helix: -0.13 (0.22), residues: 581
  sheet:  None (None), residues: 0
  loop : -2.71 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.010   0.001   PHE B 314 
 TYR   0.013   0.001   TYR A 354 
 ARG   0.008   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  335)
  hydrogen bonds       : angle       4.10478 (  996)
  SS BOND              : bond        0.00308 (    6)
  SS BOND              : angle       0.79036 (   12)
  covalent geometry    : bond        0.00227 ( 7593)
  covalent geometry    : angle       0.62709 (10323)

*********************** 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
  198 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ASN cc_start: 0.8259 (m110) cc_final: 0.7766 (m110)
REVERT: A  169 GLU cc_start: 0.7880 (tp30) cc_final: 0.7645 (tp30)
REVERT: A  173 PHE cc_start: 0.8592 (m-10) cc_final: 0.8348 (m-10)
REVERT: A  356 MET cc_start: 0.8021 (mmm) cc_final: 0.7752 (mmp)
REVERT: A  418 LEU cc_start: 0.8291 (mm) cc_final: 0.7948 (tt)
REVERT: A  444 MET cc_start: 0.8780 (tpp) cc_final: 0.8173 (tpp)
REVERT: B   14 MET cc_start: 0.8339 (mpp) cc_final: 0.7890 (mpp)
REVERT: B  163 MET cc_start: 0.7390 (mmm) cc_final: 0.7091 (mmm)
REVERT: B  286 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.7953 (m-10)
REVERT: B  356 MET cc_start: 0.8438 (mmt) cc_final: 0.8229 (mmm)
REVERT: B  456 ILE cc_start: 0.8947 (mp) cc_final: 0.8673 (mm)
REVERT: B  478 TYR cc_start: 0.8894 (t80) cc_final: 0.7962 (m-80)
  outliers start: 28
  outliers final: 14
  residues processed: 189
  average time/residue: 0.1533
  time to fit residues: 41.6775
Evaluate side-chains
  171 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  208 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  433 VAL
Chi-restraints excluded: chain A residue  476 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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 8 optimal weight:    0.2980
   chunk 17 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.6702

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN
B 315 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.148448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.115105 restraints weight = 15985.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.118535 restraints weight = 8752.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.120715 restraints weight = 5951.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7599  Z= 0.176
  Angle     :  0.693  11.398  10335  Z= 0.338
  Chirality :  0.043   0.153   1250
  Planarity :  0.004   0.059   1270
  Dihedral  :  4.798  20.786   1061
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 26.36 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.26), residues: 1003
  helix: -0.05 (0.21), residues: 587
  sheet: -3.06 (1.63), residues: 10
  loop : -2.65 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 335 
 HIS   0.009   0.002   HIS B  17 
 PHE   0.015   0.002   PHE A 308 
 TYR   0.014   0.001   TYR A 343 
 ARG   0.019   0.001   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  335)
  hydrogen bonds       : angle       4.34356 (  996)
  SS BOND              : bond        0.00348 (    6)
  SS BOND              : angle       1.15698 (   12)
  covalent geometry    : bond        0.00396 ( 7593)
  covalent geometry    : angle       0.69233 (10323)

*********************** 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
  221 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 174
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 PHE cc_start: 0.8291 (m-80) cc_final: 0.8005 (m-80)
REVERT: A  169 GLU cc_start: 0.8241 (tp30) cc_final: 0.7831 (tp30)
REVERT: A  356 MET cc_start: 0.8445 (mmm) cc_final: 0.8098 (mmp)
REVERT: A  358 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8169 (mp0)
REVERT: A  444 MET cc_start: 0.8918 (tpp) cc_final: 0.8412 (tpp)
REVERT: B  163 MET cc_start: 0.7353 (mmm) cc_final: 0.7087 (mmm)
REVERT: B  203 MET cc_start: 0.8838 (tpp) cc_final: 0.8556 (tpp)
REVERT: B  251 THR cc_start: 0.9159 (p) cc_final: 0.8706 (t)
REVERT: B  286 TRP cc_start: 0.8708 (OUTLIER) cc_final: 0.8412 (m-10)
REVERT: B  424 MET cc_start: 0.8777 (ppp) cc_final: 0.8567 (ppp)
  outliers start: 47
  outliers final: 34
  residues processed: 204
  average time/residue: 0.1565
  time to fit residues: 45.5508
Evaluate side-chains
  189 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
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  144 ILE
Chi-restraints excluded: chain A residue  208 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  338 PHE
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  445 VAL
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  476 LEU
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  161 THR
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  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  471 ILE
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 77 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0570
   chunk 88 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.4033 r_free = 0.4033 target = 0.148387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.115906 restraints weight = 15580.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.119453 restraints weight = 8480.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.121709 restraints weight = 5679.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7599  Z= 0.112
  Angle     :  0.645  11.919  10335  Z= 0.307
  Chirality :  0.041   0.166   1250
  Planarity :  0.004   0.051   1270
  Dihedral  :  4.544  20.477   1061
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.76 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.26), residues: 1003
  helix:  0.15 (0.22), residues: 587
  sheet:  None (None), residues: 0
  loop : -2.61 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.020   0.001   PHE A 173 
 TYR   0.014   0.001   TYR A 343 
 ARG   0.005   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03233 (  335)
  hydrogen bonds       : angle       3.99395 (  996)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.09127 (   12)
  covalent geometry    : bond        0.00251 ( 7593)
  covalent geometry    : angle       0.64455 (10323)

*********************** 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
  201 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 TYR cc_start: 0.8174 (t80) cc_final: 0.7905 (t80)
REVERT: A  335 TRP cc_start: 0.7669 (m-10) cc_final: 0.7114 (m-90)
REVERT: A  356 MET cc_start: 0.8441 (mmm) cc_final: 0.7999 (mmp)
REVERT: A  358 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8186 (mp0)
REVERT: A  444 MET cc_start: 0.8835 (tpp) cc_final: 0.8432 (tpp)
REVERT: B  163 MET cc_start: 0.7364 (mmm) cc_final: 0.7047 (mmm)
REVERT: B  203 MET cc_start: 0.8711 (tpp) cc_final: 0.8389 (tpp)
REVERT: B  267 MET cc_start: 0.8713 (mmm) cc_final: 0.8370 (mmm)
REVERT: B  286 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.8509 (m-10)
REVERT: B  424 MET cc_start: 0.8795 (ppp) cc_final: 0.8582 (ppp)
REVERT: B  462 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8718 (tptm)
  outliers start: 36
  outliers final: 23
  residues processed: 187
  average time/residue: 0.1610
  time to fit residues: 42.4871
Evaluate side-chains
  178 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
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 A residue  479 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain B residue   58 ILE
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  161 THR
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  281 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.141574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.108806 restraints weight = 15963.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.112060 restraints weight = 8683.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.114145 restraints weight = 5878.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7599  Z= 0.190
  Angle     :  0.705  11.273  10335  Z= 0.348
  Chirality :  0.044   0.171   1250
  Planarity :  0.004   0.050   1270
  Dihedral  :  4.964  22.087   1061
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  6.46 %
    Allowed  : 27.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.26), residues: 1003
  helix:  0.11 (0.22), residues: 589
  sheet: -3.39 (1.49), residues: 10
  loop : -2.63 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 458 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.021   0.002   PHE A 173 
 TYR   0.019   0.002   TYR A 343 
 ARG   0.004   0.001   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  335)
  hydrogen bonds       : angle       4.37082 (  996)
  SS BOND              : bond        0.00490 (    6)
  SS BOND              : angle       1.86789 (   12)
  covalent geometry    : bond        0.00428 ( 7593)
  covalent geometry    : angle       0.70221 (10323)

*********************** 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
  221 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 170
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.9430 (ptmt) cc_final: 0.9220 (ptmt)
REVERT: A   73 SER cc_start: 0.9119 (m) cc_final: 0.8841 (p)
REVERT: A  159 TYR cc_start: 0.8459 (t80) cc_final: 0.8199 (t80)
REVERT: A  213 ASN cc_start: 0.7545 (t0) cc_final: 0.7171 (t0)
REVERT: A  335 TRP cc_start: 0.7659 (m-10) cc_final: 0.7045 (m-90)
REVERT: A  356 MET cc_start: 0.8628 (mmm) cc_final: 0.8165 (mmp)
REVERT: A  358 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8307 (mp0)
REVERT: A  444 MET cc_start: 0.8957 (tpp) cc_final: 0.8540 (tpp)
REVERT: B  163 MET cc_start: 0.7261 (mmm) cc_final: 0.6885 (mmm)
REVERT: B  179 LEU cc_start: 0.8198 (pt) cc_final: 0.7128 (tp)
REVERT: B  203 MET cc_start: 0.8801 (tpp) cc_final: 0.8498 (tpp)
REVERT: B  251 THR cc_start: 0.9083 (p) cc_final: 0.8654 (t)
REVERT: B  267 MET cc_start: 0.8548 (mmm) cc_final: 0.8196 (mmm)
REVERT: B  449 MET cc_start: 0.8083 (ttm) cc_final: 0.7845 (ttp)
  outliers start: 51
  outliers final: 39
  residues processed: 202
  average time/residue: 0.1454
  time to fit residues: 42.3055
Evaluate side-chains
  203 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 164
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
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  119 VAL
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  218 LEU
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  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
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  466 THR
Chi-restraints excluded: chain A residue  476 LEU
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  161 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  195 LEU
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  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  421 LEU
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 14 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 20 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 ASN
A 306 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.145631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.113094 restraints weight = 15737.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.116482 restraints weight = 8470.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.118648 restraints weight = 5693.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4343

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= 0.114
  Angle     :  0.672  11.708  10335  Z= 0.318
  Chirality :  0.042   0.186   1250
  Planarity :  0.004   0.045   1270
  Dihedral  :  4.682  22.474   1061
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.77 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.27), residues: 1003
  helix:  0.24 (0.22), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.52 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  11 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.025   0.001   PHE A 173 
 TYR   0.016   0.001   TYR B 143 
 ARG   0.002   0.000   ARG A 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03219 (  335)
  hydrogen bonds       : angle       3.99498 (  996)
  SS BOND              : bond        0.00208 (    6)
  SS BOND              : angle       1.32547 (   12)
  covalent geometry    : bond        0.00255 ( 7593)
  covalent geometry    : angle       0.67080 (10323)

*********************** 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
  207 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 171
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.9040 (m) cc_final: 0.8725 (p)
REVERT: A  159 TYR cc_start: 0.8414 (t80) cc_final: 0.8138 (t80)
REVERT: A  335 TRP cc_start: 0.7670 (m-10) cc_final: 0.7131 (m-90)
REVERT: A  356 MET cc_start: 0.8343 (mmm) cc_final: 0.7908 (mmp)
REVERT: A  358 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8166 (mp0)
REVERT: A  444 MET cc_start: 0.8881 (tpp) cc_final: 0.8462 (tpp)
REVERT: B   36 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7564 (mtt180)
REVERT: B  163 MET cc_start: 0.7159 (mmm) cc_final: 0.6797 (mmm)
REVERT: B  203 MET cc_start: 0.8711 (tpp) cc_final: 0.8429 (tpp)
REVERT: B  251 THR cc_start: 0.9071 (p) cc_final: 0.8613 (t)
REVERT: B  267 MET cc_start: 0.8426 (mmm) cc_final: 0.8089 (mmm)
REVERT: B  449 MET cc_start: 0.8076 (ttm) cc_final: 0.7853 (ttp)
  outliers start: 36
  outliers final: 31
  residues processed: 193
  average time/residue: 0.1498
  time to fit residues: 41.5368
Evaluate side-chains
  190 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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  218 LEU
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  266 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  476 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  148 VAL
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  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  478 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0020
   chunk 10 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.146196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.113600 restraints weight = 15933.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.117041 restraints weight = 8546.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.119263 restraints weight = 5716.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7599  Z= 0.114
  Angle     :  0.660  12.012  10335  Z= 0.313
  Chirality :  0.041   0.185   1250
  Planarity :  0.004   0.046   1270
  Dihedral  :  4.527  24.684   1061
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 28.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.26), residues: 1003
  helix:  0.31 (0.22), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.59 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 335 
 HIS   0.010   0.001   HIS B  17 
 PHE   0.023   0.001   PHE A 173 
 TYR   0.016   0.001   TYR B 143 
 ARG   0.005   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03252 (  335)
  hydrogen bonds       : angle       3.95375 (  996)
  SS BOND              : bond        0.00185 (    6)
  SS BOND              : angle       0.81864 (   12)
  covalent geometry    : bond        0.00258 ( 7593)
  covalent geometry    : angle       0.66027 (10323)

*********************** 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
  199 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 168
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.8970 (m) cc_final: 0.8637 (p)
REVERT: A  159 TYR cc_start: 0.8451 (t80) cc_final: 0.8139 (t80)
REVERT: A  213 ASN cc_start: 0.7301 (t0) cc_final: 0.6856 (t0)
REVERT: A  335 TRP cc_start: 0.7665 (m-10) cc_final: 0.7111 (m-90)
REVERT: A  356 MET cc_start: 0.8391 (mmm) cc_final: 0.7979 (mmp)
REVERT: A  358 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8095 (mp0)
REVERT: A  444 MET cc_start: 0.8816 (tpp) cc_final: 0.8514 (tpp)
REVERT: B  124 MET cc_start: 0.8286 (tpp) cc_final: 0.8079 (tpp)
REVERT: B  163 MET cc_start: 0.7120 (mmm) cc_final: 0.6764 (mmm)
REVERT: B  203 MET cc_start: 0.8638 (tpp) cc_final: 0.8355 (tpp)
REVERT: B  251 THR cc_start: 0.9033 (p) cc_final: 0.8567 (t)
  outliers start: 31
  outliers final: 29
  residues processed: 186
  average time/residue: 0.1552
  time to fit residues: 41.6677
Evaluate side-chains
  192 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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  218 LEU
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  266 LEU
Chi-restraints excluded: chain A residue  279 VAL
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  445 VAL
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  476 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  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  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  477 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0370
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.147060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.115025 restraints weight = 15850.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.118544 restraints weight = 8432.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.120832 restraints weight = 5582.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7599  Z= 0.112
  Angle     :  0.683  12.468  10335  Z= 0.319
  Chirality :  0.042   0.263   1250
  Planarity :  0.004   0.063   1270
  Dihedral  :  4.444  25.299   1061
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 29.02 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.26), residues: 1003
  helix:  0.36 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.60 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.019   0.001   PHE B 132 
 TYR   0.017   0.001   TYR B 143 
 ARG   0.007   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  335)
  hydrogen bonds       : angle       3.98463 (  996)
  SS BOND              : bond        0.00208 (    6)
  SS BOND              : angle       0.78189 (   12)
  covalent geometry    : bond        0.00257 ( 7593)
  covalent geometry    : angle       0.68282 (10323)

*********************** 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
  205 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.8834 (m) cc_final: 0.8116 (p)
REVERT: A  213 ASN cc_start: 0.7121 (t0) cc_final: 0.6763 (t0)
REVERT: A  335 TRP cc_start: 0.7693 (m-10) cc_final: 0.7133 (m-90)
REVERT: A  356 MET cc_start: 0.8411 (mmm) cc_final: 0.8045 (mmp)
REVERT: A  358 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8072 (mp0)
REVERT: A  444 MET cc_start: 0.8801 (tpp) cc_final: 0.8496 (tpp)
REVERT: B   36 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7359 (mtt180)
REVERT: B  203 MET cc_start: 0.8698 (tpp) cc_final: 0.8421 (tpp)
REVERT: B  251 THR cc_start: 0.9014 (p) cc_final: 0.8531 (t)
REVERT: B  267 MET cc_start: 0.8447 (mmm) cc_final: 0.8055 (mmt)
  outliers start: 32
  outliers final: 29
  residues processed: 189
  average time/residue: 0.1546
  time to fit residues: 42.4219
Evaluate side-chains
  195 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  218 LEU
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  266 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
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  466 THR
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  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  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  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0020
   chunk 94 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.5192

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.143045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.109973 restraints weight = 16199.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.113326 restraints weight = 8755.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.115540 restraints weight = 5889.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7599  Z= 0.165
  Angle     :  0.749  12.738  10335  Z= 0.356
  Chirality :  0.044   0.281   1250
  Planarity :  0.005   0.061   1270
  Dihedral  :  4.692  25.550   1061
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 29.91 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.26), residues: 1003
  helix:  0.23 (0.21), residues: 599
  sheet:  None (None), residues: 0
  loop : -2.58 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  11 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.028   0.002   PHE B 132 
 TYR   0.016   0.001   TYR A 343 
 ARG   0.006   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  335)
  hydrogen bonds       : angle       4.25473 (  996)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       1.86975 (   12)
  covalent geometry    : bond        0.00381 ( 7593)
  covalent geometry    : angle       0.74632 (10323)

********************** 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
  208 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.8798 (m) cc_final: 0.8518 (p)
REVERT: A  213 ASN cc_start: 0.7232 (t0) cc_final: 0.6822 (t0)
REVERT: A  335 TRP cc_start: 0.7725 (m-10) cc_final: 0.7150 (m-90)
REVERT: A  356 MET cc_start: 0.8526 (mmm) cc_final: 0.8049 (mmp)
REVERT: A  444 MET cc_start: 0.8908 (tpp) cc_final: 0.8554 (tpp)
REVERT: A  466 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8896 (t)
REVERT: B  124 MET cc_start: 0.8242 (tpp) cc_final: 0.7994 (tpt)
REVERT: B  203 MET cc_start: 0.8768 (tpp) cc_final: 0.8438 (tpp)
REVERT: B  251 THR cc_start: 0.9011 (p) cc_final: 0.8562 (t)
REVERT: B  267 MET cc_start: 0.8526 (mmm) cc_final: 0.8148 (mmt)
REVERT: B  343 TYR cc_start: 0.8181 (t80) cc_final: 0.7875 (t80)
  outliers start: 32
  outliers final: 27
  residues processed: 193
  average time/residue: 0.1484
  time to fit residues: 42.3716
Evaluate side-chains
  198 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  218 LEU
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  266 LEU
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  359 ILE
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  466 THR
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  168 LEU
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  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  477 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    0.0570
   chunk 66 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.145642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.112815 restraints weight = 15990.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.116249 restraints weight = 8609.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.118478 restraints weight = 5781.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.5020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7599  Z= 0.125
  Angle     :  0.754  13.406  10335  Z= 0.350
  Chirality :  0.043   0.257   1250
  Planarity :  0.004   0.053   1270
  Dihedral  :  4.586  25.032   1061
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 31.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.26), residues: 1003
  helix:  0.24 (0.22), residues: 603
  sheet:  None (None), residues: 0
  loop : -2.59 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  11 
 HIS   0.008   0.001   HIS B  17 
 PHE   0.025   0.001   PHE B 132 
 TYR   0.020   0.001   TYR B 143 
 ARG   0.007   0.000   ARG B 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03300 (  335)
  hydrogen bonds       : angle       4.09057 (  996)
  SS BOND              : bond        0.00261 (    6)
  SS BOND              : angle       1.78518 (   12)
  covalent geometry    : bond        0.00288 ( 7593)
  covalent geometry    : angle       0.75244 (10323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2712.78 seconds
wall clock time: 47 minutes 47.83 seconds (2867.83 seconds total)