Starting phenix.real_space_refine
on Wed Sep 25 02:53:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/09_2024/6x3f_22021.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/09_2024/6x3f_22021.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/09_2024/6x3f_22021.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/09_2024/6x3f_22021.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/09_2024/6x3f_22021.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3f_22021/09_2024/6x3f_22021.cif"
  }
  resolution = 3.03
  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=   0.004
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      66      5.16       5
     C    6144      2.51       5
     N    1488      2.21       5
     O    1668      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 9366
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3115
          Classifications: {'peptide': 409}
          Link IDs: {'PTRANS': 11, 'TRANS': 397}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'CHT': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 5.94, per 1000 atoms: 0.63
  Number of scatterers: 9366
  At special positions: 0
  Unit cell: (115.648, 112.32, 77.376, 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      66     16.00
     O    1668      8.00
     N    1488      7.00
     C    6144      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.38
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 6 sheets defined
      72.9% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 40
      removed outlier: 3.711A  pdb=" N   THR A  24 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 81
      removed outlier: 3.679A  pdb=" N   LEU A  59 " --> pdb=" O   PRO A  55 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
    Processing helix  chain 'A' and resid 96 through 116
      removed outlier: 4.034A  pdb=" N   THR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE A 104 " --> pdb=" O   CYS A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.982A  pdb=" N   ASP A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   PHE A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 211 through 229
      removed outlier: 3.699A  pdb=" N   CYS A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 247
      removed outlier: 3.669A  pdb=" N   VAL A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 255
    Processing helix  chain 'A' and resid 257 through 273
      removed outlier: 3.600A  pdb=" N   PHE A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLU A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 282 through 296
      removed outlier: 3.846A  pdb=" N   MET A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   THR A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.774A  pdb=" N   VAL A 308 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 320
      removed outlier: 3.670A  pdb=" N   PHE A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   MET A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.846A  pdb=" N   MET A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 348
      removed outlier: 3.590A  pdb=" N   GLU A 345 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLU A 346 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 359
      removed outlier: 3.754A  pdb=" N   THR A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 385
      removed outlier: 3.657A  pdb=" N   ALA A 371 " --> pdb=" O   MET A 367 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 372 " --> pdb=" O   ASP A 368 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ALA A 375 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   VAL A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 408
      removed outlier: 3.728A  pdb=" N   ILE A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ILE A 406 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLY A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 426
      removed outlier: 3.583A  pdb=" N   THR A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 436
      removed outlier: 3.876A  pdb=" N   THR A 434 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A 435 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 458
      removed outlier: 4.615A  pdb=" N   ARG A 445 " --> pdb=" O   TRP A 441 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 40
      removed outlier: 3.710A  pdb=" N   THR B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG B  39 " --> pdb=" O   GLY B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 81
      removed outlier: 3.680A  pdb=" N   LEU B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU B  68 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
      Proline residue:  B  69  - end of helix
    Processing helix  chain 'B' and resid 96 through 116
      removed outlier: 4.034A  pdb=" N   THR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE B 104 " --> pdb=" O   CYS B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 150
      removed outlier: 3.982A  pdb=" N   ASP B 144 " --> pdb=" O   ASP B 140 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU B 145 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE B 146 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   PHE B 150 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 158
    Processing helix  chain 'B' and resid 211 through 229
      removed outlier: 3.699A  pdb=" N   CYS B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 247
      removed outlier: 3.668A  pdb=" N   VAL B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 255
    Processing helix  chain 'B' and resid 257 through 273
      removed outlier: 3.600A  pdb=" N   PHE B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 282
    Processing helix  chain 'B' and resid 282 through 296
      removed outlier: 3.846A  pdb=" N   MET B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   THR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 309
      removed outlier: 3.775A  pdb=" N   VAL B 308 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 320
      removed outlier: 3.669A  pdb=" N   PHE B 316 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   MET B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 331
      removed outlier: 3.846A  pdb=" N   MET B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 348
      removed outlier: 3.589A  pdb=" N   GLU B 345 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLU B 346 " --> pdb=" O   ARG B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 359
      removed outlier: 3.754A  pdb=" N   THR B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 385
      removed outlier: 3.657A  pdb=" N   ALA B 371 " --> pdb=" O   MET B 367 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU B 372 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA B 375 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   VAL B 376 " --> pdb=" O   LEU B 372 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 408
      removed outlier: 3.727A  pdb=" N   ILE B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER B 405 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ILE B 406 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLY B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 426
      removed outlier: 3.584A  pdb=" N   THR B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET B 419 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 3.875A  pdb=" N   THR B 434 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 435 " --> pdb=" O   ASP B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 458
      removed outlier: 4.614A  pdb=" N   ARG B 445 " --> pdb=" O   TRP B 441 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B 450 " --> pdb=" O   PHE B 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 40
      removed outlier: 3.711A  pdb=" N   THR C  24 " --> pdb=" O   VAL C  20 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU C  30 " --> pdb=" O   ALA C  26 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG C  39 " --> pdb=" O   GLY C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 81
      removed outlier: 3.679A  pdb=" N   LEU C  59 " --> pdb=" O   PRO C  55 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET C  60 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE C  66 " --> pdb=" O   MET C  62 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   LEU C  68 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
      Proline residue:  C  69  - end of helix
    Processing helix  chain 'C' and resid 96 through 116
      removed outlier: 4.033A  pdb=" N   THR C 102 " --> pdb=" O   TYR C  98 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE C 104 " --> pdb=" O   CYS C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 150
      removed outlier: 3.982A  pdb=" N   ASP C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU C 145 " --> pdb=" O   ALA C 141 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE C 146 " --> pdb=" O   MET C 142 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE C 150 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 158
    Processing helix  chain 'C' and resid 211 through 229
      removed outlier: 3.698A  pdb=" N   CYS C 219 " --> pdb=" O   LEU C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 247
      removed outlier: 3.669A  pdb=" N   VAL C 237 " --> pdb=" O   GLY C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 255
    Processing helix  chain 'C' and resid 257 through 273
      removed outlier: 3.600A  pdb=" N   PHE C 264 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLU C 272 " --> pdb=" O   GLY C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 282
    Processing helix  chain 'C' and resid 282 through 296
      removed outlier: 3.845A  pdb=" N   MET C 286 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   THR C 291 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA C 294 " --> pdb=" O   LEU C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 309
      removed outlier: 3.774A  pdb=" N   VAL C 308 " --> pdb=" O   ILE C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 320
      removed outlier: 3.670A  pdb=" N   PHE C 316 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   MET C 318 " --> pdb=" O   PHE C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 331
      removed outlier: 3.845A  pdb=" N   MET C 329 " --> pdb=" O   LEU C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 336 through 348
      removed outlier: 3.590A  pdb=" N   GLU C 345 " --> pdb=" O   PHE C 341 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLU C 346 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 359
      removed outlier: 3.754A  pdb=" N   THR C 355 " --> pdb=" O   ASP C 351 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE C 357 " --> pdb=" O   ARG C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 385
      removed outlier: 3.657A  pdb=" N   ALA C 371 " --> pdb=" O   MET C 367 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU C 372 " --> pdb=" O   ASP C 368 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ALA C 375 " --> pdb=" O   ALA C 371 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   VAL C 376 " --> pdb=" O   LEU C 372 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   VAL C 379 " --> pdb=" O   ALA C 375 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 408
      removed outlier: 3.727A  pdb=" N   ILE C 395 " --> pdb=" O   ILE C 391 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR C 402 " --> pdb=" O   SER C 398 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER C 405 " --> pdb=" O   ALA C 401 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ILE C 406 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLY C 407 " --> pdb=" O   SER C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 413 through 426
      removed outlier: 3.582A  pdb=" N   THR C 418 " --> pdb=" O   ALA C 414 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET C 419 " --> pdb=" O   GLY C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 436
      removed outlier: 3.876A  pdb=" N   THR C 434 " --> pdb=" O   GLU C 431 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU C 435 " --> pdb=" O   ASP C 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 458
      removed outlier: 4.614A  pdb=" N   ARG C 445 " --> pdb=" O   TRP C 441 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   PHE C 446 " --> pdb=" O   LEU C 442 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL C 450 " --> pdb=" O   PHE C 446 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161
    Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167
    Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 161
    Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 167

    517 hydrogen bonds defined for protein.
    1497 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: 2.64

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2847
        1.34 -     1.46: 1329
        1.46 -     1.57: 5208
        1.57 -     1.69: 0
        1.69 -     1.81: 117
  Bond restraints: 9501
  Sorted by residual:
  bond pdb=" C5  CHT A 601 "
       pdb=" N1  CHT A 601 "
    ideal  model  delta    sigma   weight residual
    1.509  1.456  0.053 2.00e-02 2.50e+03 7.10e+00
  bond pdb=" C5  CHT B 601 "
       pdb=" N1  CHT B 601 "
    ideal  model  delta    sigma   weight residual
    1.509  1.456  0.053 2.00e-02 2.50e+03 7.02e+00
  bond pdb=" C5  CHT C 601 "
       pdb=" N1  CHT C 601 "
    ideal  model  delta    sigma   weight residual
    1.509  1.456  0.053 2.00e-02 2.50e+03 7.01e+00
  bond pdb=" C7  CHT C 601 "
       pdb=" N1  CHT C 601 "
    ideal  model  delta    sigma   weight residual
    1.492  1.451  0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C8  CHT B 601 "
       pdb=" N1  CHT B 601 "
    ideal  model  delta    sigma   weight residual
    1.492  1.451  0.041 2.00e-02 2.50e+03 4.11e+00
  ... (remaining 9496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 12254
        1.84 -     3.67: 525
        3.67 -     5.51: 73
        5.51 -     7.34: 21
        7.34 -     9.18: 21
  Bond angle restraints: 12894
  Sorted by residual:
  angle pdb=" C   VAL C 120 "
        pdb=" N   THR C 121 "
        pdb=" CA  THR C 121 "
      ideal   model   delta    sigma   weight residual
     121.70  127.94   -6.24 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" C   VAL B 120 "
        pdb=" N   THR B 121 "
        pdb=" CA  THR B 121 "
      ideal   model   delta    sigma   weight residual
     121.70  127.91   -6.21 1.80e+00 3.09e-01 1.19e+01
  angle pdb=" C   VAL A 120 "
        pdb=" N   THR A 121 "
        pdb=" CA  THR A 121 "
      ideal   model   delta    sigma   weight residual
     121.70  127.91   -6.21 1.80e+00 3.09e-01 1.19e+01
  angle pdb=" C   ASP B 388 "
        pdb=" N   LEU B 389 "
        pdb=" CA  LEU B 389 "
      ideal   model   delta    sigma   weight residual
     121.54  127.45   -5.91 1.91e+00 2.74e-01 9.59e+00
  angle pdb=" C   ASP A 388 "
        pdb=" N   LEU A 389 "
        pdb=" CA  LEU A 389 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.53e+00
  ... (remaining 12889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5124
       17.91 -    35.83: 429
       35.83 -    53.74: 96
       53.74 -    71.65: 21
       71.65 -    89.56: 6
  Dihedral angle restraints: 5676
    sinusoidal: 2160
      harmonic: 3516
  Sorted by residual:
  dihedral pdb=" CA  VAL B 462 "
           pdb=" C   VAL B 462 "
           pdb=" N   GLU B 463 "
           pdb=" CA  GLU B 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.81   19.19     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  THR A 247 "
           pdb=" C   THR A 247 "
           pdb=" N   MET A 248 "
           pdb=" CA  MET A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.82   19.18     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  THR B 247 "
           pdb=" C   THR B 247 "
           pdb=" N   MET B 248 "
           pdb=" CA  MET B 248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.82   19.18     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5673 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1380
       0.071 -    0.143: 210
       0.143 -    0.214: 42
       0.214 -    0.286: 3
       0.286 -    0.357: 3
  Chirality restraints: 1638
  Sorted by residual:
  chirality pdb=" CB  VAL B  36 "
            pdb=" CA  VAL B  36 "
            pdb=" CG1 VAL B  36 "
            pdb=" CG2 VAL B  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CB  VAL C  36 "
            pdb=" CA  VAL C  36 "
            pdb=" CG1 VAL C  36 "
            pdb=" CG2 VAL C  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" CB  VAL A  36 "
            pdb=" CA  VAL A  36 "
            pdb=" CG1 VAL A  36 "
            pdb=" CG2 VAL A  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.15e+00
  ... (remaining 1635 not shown)

  Planarity restraints: 1563
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 258 "   -0.043 5.00e-02 4.00e+02   6.53e-02 6.83e+00
        pdb=" N   PRO B 259 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 258 "    0.043 5.00e-02 4.00e+02   6.53e-02 6.82e+00
        pdb=" N   PRO A 259 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 259 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 259 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C 258 "    0.043 5.00e-02 4.00e+02   6.53e-02 6.82e+00
        pdb=" N   PRO C 259 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 259 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 259 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1560 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 3219
        2.86 -     3.37: 8826
        3.37 -     3.88: 14813
        3.88 -     4.39: 18117
        4.39 -     4.90: 31053
  Nonbonded interactions: 76028
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD1 ASP B 455 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OH  TYR A  98 "
            pdb=" OD1 ASP A 455 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OH  TYR C  98 "
            pdb=" OD1 ASP C 455 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OH  TYR C 373 "
            pdb=" OD1 ASP C 440 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OH  TYR A 373 "
            pdb=" OD1 ASP A 440 "
     model   vdw
     2.369 3.040
  ... (remaining 76023 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.290
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
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      :  0.006   0.055   9501  Z= 0.385
  Angle     :  0.934   9.177  12894  Z= 0.489
  Chirality :  0.058   0.357   1638
  Planarity :  0.008   0.065   1563
  Dihedral  : 14.719  89.564   3408
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.51 %
    Favored  : 86.49 %
  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: -6.78 (0.13), residues: 1209
  helix: -4.59 (0.07), residues: 933
  sheet: -3.31 (0.65), residues: 54
  loop : -2.49 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 441 
 HIS   0.001   0.001   HIS C  41 
 PHE   0.011   0.002   PHE C 159 
 TYR   0.012   0.002   TYR C 162 
 ARG   0.005   0.001   ARG A 353 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A  149 MET cc_start: 0.8776 (mtt) cc_final: 0.8543 (mtp)
REVERT: A  163 LYS cc_start: 0.8467 (tttm) cc_final: 0.8119 (tptp)
REVERT: B  149 MET cc_start: 0.8755 (mtt) cc_final: 0.8534 (mtp)
REVERT: B  163 LYS cc_start: 0.8481 (tttm) cc_final: 0.8244 (tmtt)
REVERT: B  280 ARG cc_start: 0.6785 (ttt180) cc_final: 0.6295 (ttp-110)
REVERT: B  306 PHE cc_start: 0.7504 (t80) cc_final: 0.7286 (t80)
REVERT: B  307 ILE cc_start: 0.8214 (mm) cc_final: 0.8013 (mt)
REVERT: C  149 MET cc_start: 0.8729 (mtt) cc_final: 0.8483 (mtp)
REVERT: C  280 ARG cc_start: 0.6844 (ttt180) cc_final: 0.6472 (ttp-110)
REVERT: C  307 ILE cc_start: 0.8236 (mm) cc_final: 0.7984 (mt)
REVERT: C  342 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7013 (ttp-170)
REVERT: C  445 ARG cc_start: 0.7729 (mpt180) cc_final: 0.7518 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2373
  time to fit residues: 55.0619
Evaluate side-chains
  143 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 108 optimal weight:    0.1980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
A 385 ASN
A 413 GLN
B 347 ASN
B 385 ASN
B 413 GLN
C 347 ASN
C 385 ASN
C 413 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9501  Z= 0.217
  Angle     :  0.594   6.576  12894  Z= 0.311
  Chirality :  0.041   0.142   1638
  Planarity :  0.006   0.042   1563
  Dihedral  :  5.351  19.903   1293
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.16 %
    Favored  : 81.92 %
  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: -4.49 (0.19), residues: 1209
  helix: -2.71 (0.13), residues: 948
  sheet: -3.12 (0.65), residues: 54
  loop : -2.76 (0.35), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 441 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.022   0.002   PHE A 306 
 TYR   0.006   0.001   TYR A 285 
 ARG   0.006   0.001   ARG A 353 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 1.169 
Fit side-chains
REVERT: A  149 MET cc_start: 0.8690 (mtt) cc_final: 0.8485 (mtp)
REVERT: A  163 LYS cc_start: 0.8587 (tttm) cc_final: 0.8237 (tmtt)
REVERT: A  262 ILE cc_start: 0.8023 (tt) cc_final: 0.7556 (pt)
REVERT: A  367 MET cc_start: 0.7200 (mtm) cc_final: 0.6988 (mtm)
REVERT: B  149 MET cc_start: 0.8654 (mtt) cc_final: 0.8433 (mtp)
REVERT: B  280 ARG cc_start: 0.6891 (ttt180) cc_final: 0.6375 (ttp-110)
REVERT: B  325 LEU cc_start: 0.7616 (tt) cc_final: 0.6593 (mp)
REVERT: B  329 MET cc_start: 0.6879 (mmt) cc_final: 0.6667 (mmm)
REVERT: B  367 MET cc_start: 0.7309 (mtm) cc_final: 0.7097 (mtm)
REVERT: C   21 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7285 (tp)
REVERT: C  149 MET cc_start: 0.8719 (mtt) cc_final: 0.8492 (mtp)
REVERT: C  280 ARG cc_start: 0.6886 (ttt180) cc_final: 0.6504 (ttp-110)
REVERT: C  298 ILE cc_start: 0.8681 (mm) cc_final: 0.8408 (mp)
REVERT: C  325 LEU cc_start: 0.7490 (tt) cc_final: 0.6731 (mp)
REVERT: C  342 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7277 (ttp-170)
  outliers start: 30
  outliers final: 17
  residues processed: 175
  average time/residue: 0.2384
  time to fit residues: 56.3189
Evaluate side-chains
  157 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  461 ILE
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  304 ILE
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  461 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 109 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0670
   chunk 37 optimal weight:    0.5980
   chunk 87 optimal weight:    7.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9501  Z= 0.155
  Angle     :  0.530   8.139  12894  Z= 0.272
  Chirality :  0.039   0.125   1638
  Planarity :  0.004   0.031   1563
  Dihedral  :  4.805  17.382   1293
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.72 %
    Favored  : 81.24 %
  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: -2.75 (0.23), residues: 1209
  helix: -1.42 (0.16), residues: 957
  sheet: -2.68 (0.69), residues: 54
  loop : -2.46 (0.38), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 441 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.020   0.001   PHE B 306 
 TYR   0.009   0.001   TYR C 285 
 ARG   0.008   0.001   ARG B 353 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  163 LYS cc_start: 0.8588 (tttm) cc_final: 0.8362 (tptp)
REVERT: A  367 MET cc_start: 0.7137 (mtm) cc_final: 0.6895 (mtm)
REVERT: B   41 HIS cc_start: 0.7057 (t70) cc_final: 0.6731 (m-70)
REVERT: B  149 MET cc_start: 0.8550 (mtt) cc_final: 0.8346 (mtp)
REVERT: B  280 ARG cc_start: 0.6859 (ttt180) cc_final: 0.6394 (ttp-110)
REVERT: B  342 ARG cc_start: 0.7477 (ttp80) cc_final: 0.7127 (ttp80)
REVERT: B  367 MET cc_start: 0.7325 (mtm) cc_final: 0.7090 (mtm)
REVERT: C   21 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7274 (tp)
REVERT: C   41 HIS cc_start: 0.6804 (t70) cc_final: 0.6597 (m-70)
REVERT: C  149 MET cc_start: 0.8622 (mtt) cc_final: 0.8397 (mtp)
REVERT: C  325 LEU cc_start: 0.7316 (tt) cc_final: 0.6550 (mp)
REVERT: C  342 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7365 (ttp-170)
  outliers start: 21
  outliers final: 14
  residues processed: 156
  average time/residue: 0.2113
  time to fit residues: 45.9835
Evaluate side-chains
  152 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  304 ILE
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  461 ILE
Chi-restraints excluded: chain C residue  462 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 312 ASN
C 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9501  Z= 0.158
  Angle     :  0.509   8.315  12894  Z= 0.260
  Chirality :  0.039   0.117   1638
  Planarity :  0.004   0.029   1563
  Dihedral  :  4.558  16.254   1293
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.37 %
    Favored  : 79.88 %
  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: -1.97 (0.24), residues: 1209
  helix: -0.87 (0.17), residues: 960
  sheet: -2.56 (0.71), residues: 54
  loop : -2.20 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 441 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.016   0.001   PHE C 306 
 TYR   0.007   0.001   TYR B 285 
 ARG   0.007   0.000   ARG B 353 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A  163 LYS cc_start: 0.8616 (tttm) cc_final: 0.8397 (tptp)
REVERT: A  367 MET cc_start: 0.7096 (mtm) cc_final: 0.6867 (mtm)
REVERT: B  262 ILE cc_start: 0.7808 (tt) cc_final: 0.7534 (tt)
REVERT: B  280 ARG cc_start: 0.6876 (ttt180) cc_final: 0.6418 (ttp-110)
REVERT: B  342 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7187 (ttp80)
REVERT: B  367 MET cc_start: 0.7291 (mtm) cc_final: 0.7064 (mtm)
REVERT: C   21 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7240 (tp)
REVERT: C  149 MET cc_start: 0.8574 (mtt) cc_final: 0.8368 (mtp)
REVERT: C  342 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7139 (ttp-170)
  outliers start: 18
  outliers final: 12
  residues processed: 152
  average time/residue: 0.2029
  time to fit residues: 44.1355
Evaluate side-chains
  146 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 0 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
C  41 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9501  Z= 0.179
  Angle     :  0.509   7.152  12894  Z= 0.259
  Chirality :  0.039   0.118   1638
  Planarity :  0.003   0.027   1563
  Dihedral  :  4.457  16.416   1293
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.85 %
    Favored  : 79.30 %
  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: -1.42 (0.25), residues: 1209
  helix: -0.51 (0.18), residues: 948
  sheet: -2.39 (0.73), residues: 54
  loop : -1.76 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 441 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.012   0.001   PHE C 306 
 TYR   0.006   0.001   TYR B 285 
 ARG   0.007   0.000   ARG C 353 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.089 
Fit side-chains
REVERT: A  163 LYS cc_start: 0.8567 (tttm) cc_final: 0.8363 (tptp)
REVERT: A  262 ILE cc_start: 0.7855 (tt) cc_final: 0.7392 (tt)
REVERT: B  262 ILE cc_start: 0.7929 (tt) cc_final: 0.7644 (tt)
REVERT: B  307 ILE cc_start: 0.8178 (mm) cc_final: 0.7960 (mt)
REVERT: B  342 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7225 (ttp80)
REVERT: B  353 ARG cc_start: 0.6061 (mtm180) cc_final: 0.5227 (mtm-85)
REVERT: B  367 MET cc_start: 0.7321 (mtm) cc_final: 0.7114 (mtm)
REVERT: B  446 PHE cc_start: 0.8102 (m-80) cc_final: 0.7802 (m-80)
REVERT: C   21 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7197 (tp)
REVERT: C  149 MET cc_start: 0.8586 (mtt) cc_final: 0.8376 (mtp)
REVERT: C  341 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6364 (m-80)
REVERT: C  342 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7099 (ttp-170)
REVERT: C  353 ARG cc_start: 0.5465 (mtm-85) cc_final: 0.5253 (mtm-85)
  outliers start: 19
  outliers final: 14
  residues processed: 148
  average time/residue: 0.1811
  time to fit residues: 39.5423
Evaluate side-chains
  147 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  461 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 116 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9501  Z= 0.204
  Angle     :  0.519   6.311  12894  Z= 0.262
  Chirality :  0.040   0.122   1638
  Planarity :  0.003   0.026   1563
  Dihedral  :  4.452  19.262   1293
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 19.24 %
    Favored  : 79.11 %
  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: -1.15 (0.25), residues: 1209
  helix: -0.34 (0.18), residues: 948
  sheet: -2.30 (0.73), residues: 54
  loop : -1.56 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  19 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.012   0.001   PHE C 240 
 TYR   0.010   0.001   TYR B 285 
 ARG   0.005   0.000   ARG C 353 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 1.147 
Fit side-chains
REVERT: A  262 ILE cc_start: 0.7942 (tt) cc_final: 0.7468 (tt)
REVERT: A  341 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.6427 (m-80)
REVERT: B  262 ILE cc_start: 0.7930 (tt) cc_final: 0.7595 (tt)
REVERT: B  307 ILE cc_start: 0.8192 (mm) cc_final: 0.7980 (mt)
REVERT: B  353 ARG cc_start: 0.6159 (mtm180) cc_final: 0.5306 (mtm-85)
REVERT: B  367 MET cc_start: 0.7332 (mtm) cc_final: 0.7126 (mtm)
REVERT: C   21 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7163 (tp)
REVERT: C  149 MET cc_start: 0.8583 (mtt) cc_final: 0.8368 (mtp)
REVERT: C  262 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7605 (tt)
REVERT: C  341 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6413 (m-80)
REVERT: C  342 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7127 (ttp-170)
  outliers start: 17
  outliers final: 12
  residues processed: 148
  average time/residue: 0.1805
  time to fit residues: 39.1946
Evaluate side-chains
  149 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  262 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 115 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9501  Z= 0.161
  Angle     :  0.493   5.907  12894  Z= 0.250
  Chirality :  0.039   0.120   1638
  Planarity :  0.003   0.025   1563
  Dihedral  :  4.301  20.160   1293
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.14 %
    Favored  : 78.23 %
  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: -0.89 (0.25), residues: 1209
  helix: -0.15 (0.18), residues: 960
  sheet: -2.23 (0.75), residues: 54
  loop : -1.57 (0.42), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 441 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.010   0.001   PHE A 240 
 TYR   0.007   0.001   TYR B 285 
 ARG   0.003   0.000   ARG C  39 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  262 ILE cc_start: 0.7937 (tt) cc_final: 0.7452 (tt)
REVERT: A  341 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.6386 (m-80)
REVERT: B  341 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.6293 (m-80)
REVERT: B  353 ARG cc_start: 0.6176 (mtm180) cc_final: 0.5323 (mtm-85)
REVERT: B  432 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8437 (m-30)
REVERT: C   21 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7156 (tp)
REVERT: C  149 MET cc_start: 0.8560 (mtt) cc_final: 0.8348 (mtp)
REVERT: C  262 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7616 (tt)
REVERT: C  341 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6388 (m-80)
  outliers start: 27
  outliers final: 18
  residues processed: 155
  average time/residue: 0.1656
  time to fit residues: 38.6235
Evaluate side-chains
  157 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  262 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   chunk 90 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9501  Z= 0.163
  Angle     :  0.502   6.666  12894  Z= 0.253
  Chirality :  0.039   0.120   1638
  Planarity :  0.003   0.025   1563
  Dihedral  :  4.254  20.495   1293
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 20.02 %
    Favored  : 77.65 %
  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: -0.73 (0.25), residues: 1209
  helix: -0.03 (0.18), residues: 963
  sheet: -2.21 (0.75), residues: 54
  loop : -1.52 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 441 
 HIS   0.001   0.000   HIS C  41 
 PHE   0.011   0.001   PHE A 341 
 TYR   0.011   0.001   TYR B 285 
 ARG   0.002   0.000   ARG C  39 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 1.070 
Fit side-chains
REVERT: A  262 ILE cc_start: 0.7931 (tt) cc_final: 0.7451 (tt)
REVERT: B  262 ILE cc_start: 0.7885 (tt) cc_final: 0.7500 (tt)
REVERT: B  341 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.6235 (m-80)
REVERT: B  353 ARG cc_start: 0.6174 (mtm180) cc_final: 0.5329 (mtm-85)
REVERT: B  432 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8476 (m-30)
REVERT: C   21 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7136 (tp)
REVERT: C  149 MET cc_start: 0.8563 (mtt) cc_final: 0.8351 (mtp)
REVERT: C  262 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7635 (tt)
REVERT: C  341 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6391 (m-80)
  outliers start: 24
  outliers final: 16
  residues processed: 151
  average time/residue: 0.1760
  time to fit residues: 39.3298
Evaluate side-chains
  153 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  262 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    4.9990
   chunk 101 optimal weight:    0.3980
   chunk 107 optimal weight:    8.9990
   chunk 64 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 113 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9501  Z= 0.158
  Angle     :  0.497   5.583  12894  Z= 0.252
  Chirality :  0.039   0.119   1638
  Planarity :  0.003   0.025   1563
  Dihedral  :  4.216  20.820   1293
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 19.92 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.59 (0.26), residues: 1209
  helix:  0.06 (0.18), residues: 981
  sheet: -2.20 (0.75), residues: 54
  loop : -1.58 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 441 
 HIS   0.001   0.000   HIS C 296 
 PHE   0.022   0.001   PHE A 341 
 TYR   0.019   0.001   TYR B 285 
 ARG   0.003   0.000   ARG C  39 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A  262 ILE cc_start: 0.7924 (tt) cc_final: 0.7425 (tt)
REVERT: B  341 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.6247 (m-80)
REVERT: B  353 ARG cc_start: 0.6156 (mtm180) cc_final: 0.5328 (mtm-85)
REVERT: B  432 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8501 (m-30)
REVERT: C   21 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7136 (tp)
REVERT: C  262 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7655 (tt)
  outliers start: 22
  outliers final: 18
  residues processed: 148
  average time/residue: 0.1809
  time to fit residues: 39.4423
Evaluate side-chains
  151 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  262 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 119 optimal weight:    0.7980
   chunk 110 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9501  Z= 0.169
  Angle     :  0.511   7.311  12894  Z= 0.256
  Chirality :  0.039   0.119   1638
  Planarity :  0.003   0.025   1563
  Dihedral  :  4.214  21.088   1293
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.63 %
    Favored  : 78.33 %
  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: -0.51 (0.26), residues: 1209
  helix:  0.12 (0.18), residues: 981
  sheet: -2.19 (0.75), residues: 54
  loop : -1.59 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 441 
 HIS   0.001   0.000   HIS C 296 
 PHE   0.018   0.001   PHE A 341 
 TYR   0.014   0.001   TYR B 285 
 ARG   0.004   0.000   ARG A 342 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.086 
Fit side-chains
REVERT: A  262 ILE cc_start: 0.7937 (tt) cc_final: 0.7459 (tt)
REVERT: B  341 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.6268 (m-80)
REVERT: B  353 ARG cc_start: 0.6161 (mtm180) cc_final: 0.5328 (mtm-85)
REVERT: B  432 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8496 (m-30)
REVERT: C   21 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7116 (tp)
REVERT: C  262 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7745 (tt)
  outliers start: 21
  outliers final: 17
  residues processed: 142
  average time/residue: 0.1804
  time to fit residues: 38.0144
Evaluate side-chains
  146 residues out of total 1029 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  328 LEU
Chi-restraints excluded: chain B residue  341 PHE
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  262 ILE
Chi-restraints excluded: chain C residue  328 LEU
Chi-restraints excluded: chain C residue  406 ILE
Chi-restraints excluded: chain C residue  411 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 95 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0470
   chunk 5 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.149845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.104089 restraints weight = 9942.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.93
r_work: 0.2932 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9501  Z= 0.146
  Angle     :  0.496   6.726  12894  Z= 0.249
  Chirality :  0.039   0.117   1638
  Planarity :  0.003   0.025   1563
  Dihedral  :  4.126  20.783   1293
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.53 %
    Favored  : 78.23 %
  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: -0.31 (0.26), residues: 1209
  helix:  0.27 (0.18), residues: 981
  sheet: -2.20 (0.75), residues: 54
  loop : -1.56 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 441 
 HIS   0.001   0.000   HIS C 296 
 PHE   0.017   0.001   PHE A 341 
 TYR   0.012   0.001   TYR B 285 
 ARG   0.004   0.000   ARG A 342 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2175.33 seconds
wall clock time: 39 minutes 40.60 seconds (2380.60 seconds total)