Starting phenix.real_space_refine
on Wed Mar  4 01:57:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iet_35393/03_2026/8iet_35393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iet_35393/03_2026/8iet_35393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iet_35393/03_2026/8iet_35393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iet_35393/03_2026/8iet_35393.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iet_35393/03_2026/8iet_35393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iet_35393/03_2026/8iet_35393.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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      38      5.16       5
     C    6700      2.51       5
     N    1670      2.21       5
     O    1776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10184
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 653, 5092
          Classifications: {'peptide': 653}
          Link IDs: {'PTRANS': 28, 'TRANS': 624}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 5092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 653, 5092
          Classifications: {'peptide': 653}
          Link IDs: {'PTRANS': 28, 'TRANS': 624}
          Chain breaks: 4
  Time building chain proxies: 2.33, per 1000 atoms: 0.23
  Number of scatterers: 10184
  At special positions: 0
  Unit cell: (102.315, 115.239, 103.392, 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      38     16.00
     O    1776      8.00
     N    1670      7.00
     C    6700      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: 0.81
  Conformation dependent library (CDL) restraints added in 512.4 milliseconds
  

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2440

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 8 sheets defined
      52.4% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 58
      removed outlier: 4.061A  pdb=" N   SER A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 62
    Processing helix  chain 'A' and resid 68 through 73
      removed outlier: 3.603A  pdb=" N   LEU A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 82
      removed outlier: 3.796A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER A  79 " --> pdb=" O   SER A  75 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLY A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER A  82 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 95
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 110 through 120
      removed outlier: 3.542A  pdb=" N   ILE A 115 " --> pdb=" O   PHE A 111 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU A 117 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   PHE A 118 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 146
      removed outlier: 4.078A  pdb=" N   SER A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   SER A 146 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 180
      removed outlier: 3.619A  pdb=" N   ALA A 177 " --> pdb=" O   ARG A 173 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ALA A 178 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 192
      removed outlier: 3.954A  pdb=" N   GLN A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 205
      removed outlier: 3.707A  pdb=" N   LEU A 205 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 225
      removed outlier: 4.116A  pdb=" N   THR A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL A 219 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS A 220 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU A 222 " --> pdb=" O   ALA A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
      removed outlier: 3.831A  pdb=" N   ILE A 229 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE A 230 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 225 through 230'
    Processing helix  chain 'A' and resid 242 through 251
      removed outlier: 3.538A  pdb=" N   VAL A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 257
      removed outlier: 4.093A  pdb=" N   THR A 257 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 282
      removed outlier: 3.738A  pdb=" N   SER A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 304
      removed outlier: 4.594A  pdb=" N   THR A 297 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE A 299 " --> pdb=" O   ILE A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 339
      removed outlier: 3.564A  pdb=" N   PHE A 336 " --> pdb=" O   ASP A 332 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ASN A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 347
      removed outlier: 3.521A  pdb=" N   ALA A 347 " --> pdb=" O   CYS A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.593A  pdb=" N   ALA A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER A 359 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A 364 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 377
    Processing helix  chain 'A' and resid 380 through 388
      removed outlier: 3.921A  pdb=" N   GLY A 386 " --> pdb=" O   ASN A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 407
      removed outlier: 3.523A  pdb=" N   ALA A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   VAL A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY A 407 " --> pdb=" O   GLN A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.592A  pdb=" N   ALA A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.623A  pdb=" N   PHE A 455 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ALA A 456 " --> pdb=" O   MET A 453 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 452 through 456'
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.518A  pdb=" N   TRP A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 483
      removed outlier: 3.512A  pdb=" N   ILE A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 496
      removed outlier: 3.692A  pdb=" N   PHE A 494 " --> pdb=" O   ALA A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 548 through 557
    Processing helix  chain 'A' and resid 565 through 580
      removed outlier: 3.546A  pdb=" N   ARG A 571 " --> pdb=" O   ILE A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 616
    Processing helix  chain 'A' and resid 660 through 676
      removed outlier: 3.616A  pdb=" N   ARG A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLY A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER A 669 " --> pdb=" O   ARG A 665 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE A 674 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 676 " --> pdb=" O   GLN A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 695
      removed outlier: 3.739A  pdb=" N   ILE A 691 " --> pdb=" O   ASP A 687 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A 694 " --> pdb=" O   PHE A 690 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASN A 695 " --> pdb=" O   ILE A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 721
    Processing helix  chain 'B' and resid 50 through 58
      removed outlier: 4.061A  pdb=" N   SER B  56 " --> pdb=" O   ARG B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 62
    Processing helix  chain 'B' and resid 68 through 73
      removed outlier: 3.603A  pdb=" N   LEU B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 82
      removed outlier: 3.796A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER B  79 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLY B  80 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER B  82 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 95
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 110 through 120
      removed outlier: 3.542A  pdb=" N   ILE B 115 " --> pdb=" O   PHE B 111 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU B 117 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   PHE B 118 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 146
      removed outlier: 4.078A  pdb=" N   SER B 142 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   SER B 146 " --> pdb=" O   SER B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 180
      removed outlier: 3.619A  pdb=" N   ALA B 177 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ALA B 178 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 192
      removed outlier: 3.954A  pdb=" N   GLN B 190 " --> pdb=" O   SER B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 205
      removed outlier: 3.707A  pdb=" N   LEU B 205 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 225
      removed outlier: 4.116A  pdb=" N   THR B 215 " --> pdb=" O   SER B 211 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL B 219 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS B 220 " --> pdb=" O   ALA B 216 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 222 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 230
      removed outlier: 3.831A  pdb=" N   ILE B 229 " --> pdb=" O   GLN B 225 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE B 230 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 225 through 230'
    Processing helix  chain 'B' and resid 242 through 251
      removed outlier: 3.537A  pdb=" N   VAL B 246 " --> pdb=" O   SER B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 257
      removed outlier: 4.093A  pdb=" N   THR B 257 " --> pdb=" O   ILE B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 282
      removed outlier: 3.738A  pdb=" N   SER B 273 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN B 280 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 304
      removed outlier: 4.594A  pdb=" N   THR B 297 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 299 " --> pdb=" O   ILE B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 339
      removed outlier: 3.564A  pdb=" N   PHE B 336 " --> pdb=" O   ASP B 332 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ASN B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR B 339 " --> pdb=" O   THR B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 347
      removed outlier: 3.521A  pdb=" N   ALA B 347 " --> pdb=" O   CYS B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 366
      removed outlier: 3.593A  pdb=" N   ALA B 358 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER B 359 " --> pdb=" O   PHE B 355 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR B 361 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 363 " --> pdb=" O   SER B 359 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS B 364 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 377
    Processing helix  chain 'B' and resid 380 through 388
      removed outlier: 3.921A  pdb=" N   GLY B 386 " --> pdb=" O   ASN B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 407
      removed outlier: 3.523A  pdb=" N   ALA B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   VAL B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY B 407 " --> pdb=" O   GLN B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 427
    Processing helix  chain 'B' and resid 439 through 444
      removed outlier: 3.592A  pdb=" N   ALA B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 456
      removed outlier: 3.623A  pdb=" N   PHE B 455 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ALA B 456 " --> pdb=" O   MET B 453 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 452 through 456'
    Processing helix  chain 'B' and resid 457 through 462
      removed outlier: 3.518A  pdb=" N   TRP B 462 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 483
      removed outlier: 3.512A  pdb=" N   ILE B 480 " --> pdb=" O   PHE B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 496
      removed outlier: 3.692A  pdb=" N   PHE B 494 " --> pdb=" O   ALA B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 499
      No H-bonds generated for 'chain 'B' and resid 497 through 499'
    Processing helix  chain 'B' and resid 548 through 557
    Processing helix  chain 'B' and resid 565 through 580
      removed outlier: 3.546A  pdb=" N   ARG B 571 " --> pdb=" O   ILE B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 616
    Processing helix  chain 'B' and resid 660 through 676
      removed outlier: 3.616A  pdb=" N   ARG B 665 " --> pdb=" O   VAL B 661 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLY B 666 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER B 669 " --> pdb=" O   ARG B 665 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B 674 " --> pdb=" O   ILE B 670 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG B 676 " --> pdb=" O   GLN B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 695
      removed outlier: 3.739A  pdb=" N   ILE B 691 " --> pdb=" O   ASP B 687 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B 694 " --> pdb=" O   PHE B 690 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASN B 695 " --> pdb=" O   ILE B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 721
    Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 522
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
      removed outlier: 3.909A  pdb=" N   ARG A 539 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   PHE A 538 " --> pdb=" O   ASP A 652 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 649
    Processing sheet with id=AA4, first strand: chain 'A' and resid 683 through 684
      removed outlier: 6.736A  pdb=" N   ILE A 683 " --> pdb=" O   PHE A 710 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522
    Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 522
      removed outlier: 3.909A  pdb=" N   ARG B 539 " --> pdb=" O   SER B 509 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   PHE B 538 " --> pdb=" O   ASP B 652 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 648 through 649
    Processing sheet with id=AA8, first strand: chain 'B' and resid 683 through 684
      removed outlier: 6.736A  pdb=" N   ILE B 683 " --> pdb=" O   PHE B 710 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    312 hydrogen bonds defined for protein.
    876 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: 1.84

  Time building geometry restraints manager: 1.15 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: 3146
        1.34 -     1.46: 2041
        1.46 -     1.58: 5157
        1.58 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 10402
  Sorted by residual:
  bond pdb=" C   ASP B 239 "
       pdb=" N   PRO B 240 "
    ideal  model  delta    sigma   weight residual
    1.331  1.394 -0.063 1.21e-02 6.83e+03 2.72e+01
  bond pdb=" C   ASP A 239 "
       pdb=" N   PRO A 240 "
    ideal  model  delta    sigma   weight residual
    1.331  1.394 -0.063 1.21e-02 6.83e+03 2.68e+01
  bond pdb=" N   PRO A 240 "
       pdb=" CD  PRO A 240 "
    ideal  model  delta    sigma   weight residual
    1.473  1.528 -0.055 1.40e-02 5.10e+03 1.56e+01
  bond pdb=" N   PRO B 240 "
       pdb=" CD  PRO B 240 "
    ideal  model  delta    sigma   weight residual
    1.473  1.527 -0.054 1.40e-02 5.10e+03 1.51e+01
  bond pdb=" CA  ASP B 239 "
       pdb=" C   ASP B 239 "
    ideal  model  delta    sigma   weight residual
    1.524  1.545 -0.021 1.26e-02 6.30e+03 2.88e+00
  ... (remaining 10397 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 13872
        2.78 -     5.56: 226
        5.56 -     8.34: 6
        8.34 -    11.12: 6
       11.12 -    13.90: 2
  Bond angle restraints: 14112
  Sorted by residual:
  angle pdb=" N   THR A 238 "
        pdb=" CA  THR A 238 "
        pdb=" C   THR A 238 "
      ideal   model   delta    sigma   weight residual
     110.80  121.50  -10.70 2.13e+00 2.20e-01 2.52e+01
  angle pdb=" N   THR B 238 "
        pdb=" CA  THR B 238 "
        pdb=" C   THR B 238 "
      ideal   model   delta    sigma   weight residual
     110.80  121.31  -10.51 2.13e+00 2.20e-01 2.44e+01
  angle pdb=" C   ASP B 239 "
        pdb=" N   PRO B 240 "
        pdb=" CA  PRO B 240 "
      ideal   model   delta    sigma   weight residual
     120.11  114.59    5.52 1.12e+00 7.97e-01 2.43e+01
  angle pdb=" C   ASP A 239 "
        pdb=" N   PRO A 240 "
        pdb=" CA  PRO A 240 "
      ideal   model   delta    sigma   weight residual
     120.11  114.60    5.51 1.12e+00 7.97e-01 2.42e+01
  angle pdb=" C   SER A  17 "
        pdb=" N   THR A  18 "
        pdb=" CA  THR A  18 "
      ideal   model   delta    sigma   weight residual
     121.54  130.88   -9.34 1.91e+00 2.74e-01 2.39e+01
  ... (remaining 14107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 5425
       16.29 -    32.58: 627
       32.58 -    48.87: 105
       48.87 -    65.16: 15
       65.16 -    81.45: 4
  Dihedral angle restraints: 6176
    sinusoidal: 2400
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CA  LEU A 435 "
           pdb=" C   LEU A 435 "
           pdb=" N   GLN A 436 "
           pdb=" CA  GLN A 436 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.67  -27.33     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  LEU B 435 "
           pdb=" C   LEU B 435 "
           pdb=" N   GLN B 436 "
           pdb=" CA  GLN B 436 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.67  -27.33     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  SER A 438 "
           pdb=" C   SER A 438 "
           pdb=" N   VAL A 439 "
           pdb=" CA  VAL A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 6173 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1489
       0.079 -    0.157: 185
       0.157 -    0.236: 4
       0.236 -    0.315: 0
       0.315 -    0.393: 4
  Chirality restraints: 1682
  Sorted by residual:
  chirality pdb=" CA  ASP B 239 "
            pdb=" N   ASP B 239 "
            pdb=" C   ASP B 239 "
            pdb=" CB  ASP B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" CA  ASP A 239 "
            pdb=" N   ASP A 239 "
            pdb=" C   ASP A 239 "
            pdb=" CB  ASP A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.43e+00
  chirality pdb=" CA  THR B 238 "
            pdb=" N   THR B 238 "
            pdb=" C   THR B 238 "
            pdb=" CB  THR B 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.21    0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 1679 not shown)

  Planarity restraints: 1750
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 100 "    0.049 5.00e-02 4.00e+02   7.32e-02 8.57e+00
        pdb=" N   PRO B 101 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 101 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 101 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 100 "    0.049 5.00e-02 4.00e+02   7.32e-02 8.57e+00
        pdb=" N   PRO A 101 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 101 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 101 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 433 "    0.039 5.00e-02 4.00e+02   5.79e-02 5.36e+00
        pdb=" N   PRO A 434 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 434 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 434 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1747 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1250
        2.75 -     3.28: 9001
        3.28 -     3.82: 15215
        3.82 -     4.36: 19244
        4.36 -     4.90: 33420
  Nonbonded interactions: 78130
  Sorted by model distance:
  nonbonded pdb=" O   THR A 238 "
            pdb=" O   ASP A 239 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   THR B 238 "
            pdb=" O   ASP B 239 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   GLY B 487 "
            pdb=" OG  SER B 491 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" O   GLY A 487 "
            pdb=" OG  SER A 491 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OD1 ASP A 465 "
            pdb=" OH  TYR B 697 "
     model   vdw
     2.339 3.040
  ... (remaining 78125 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.180
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:1.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
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   0.063  10402  Z= 0.271
  Angle     :  0.879  13.898  14112  Z= 0.493
  Chirality :  0.055   0.393   1682
  Planarity :  0.007   0.073   1750
  Dihedral  : 13.904  81.452   3736
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.91 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  8.41 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.60 (0.14), residues: 1286
  helix: -5.02 (0.05), residues: 734
  sheet: -1.99 (0.87), residues: 36
  loop : -3.26 (0.21), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 539 
 TYR   0.022   0.002   TYR A   9 
 PHE   0.022   0.002   PHE A 130 
 TRP   0.034   0.003   TRP B 472 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (10402)
  covalent geometry    : angle       0.87923 (14112)
  hydrogen bonds       : bond        0.32578 (  308)
  hydrogen bonds       : angle      11.44325 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 168
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6605 (tp-100)
REVERT: A   55 LEU cc_start: 0.8360 (mp) cc_final: 0.7939 (tt)
REVERT: A  293 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6512 (tt0)
REVERT: A  363 LEU cc_start: 0.8131 (mp) cc_final: 0.7868 (mp)
REVERT: A  612 GLN cc_start: 0.7483 (mt0) cc_final: 0.6735 (mt0)
REVERT: B   48 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6618 (tp-100)
REVERT: B   55 LEU cc_start: 0.8357 (mp) cc_final: 0.7939 (tt)
REVERT: B  293 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6511 (tt0)
REVERT: B  363 LEU cc_start: 0.8121 (mp) cc_final: 0.7862 (mp)
REVERT: B  612 GLN cc_start: 0.7490 (mt0) cc_final: 0.6743 (mt0)
  outliers start: 5
  outliers final: 3
  residues processed: 171
  average time/residue: 0.1085
  time to fit residues: 25.8358
Evaluate side-chains
  113 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  320 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 129 optimal weight:    0.5980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A 447 ASN
A 454 GLN
A 495 GLN
A 504 GLN
B 447 ASN
B 454 GLN
B 495 GLN
B 504 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.139162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.116690 restraints weight = 11928.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.115923 restraints weight = 14001.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.116702 restraints weight = 11830.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.117178 restraints weight = 9547.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.117402 restraints weight = 8592.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10402  Z= 0.128
  Angle     :  0.577   7.473  14112  Z= 0.309
  Chirality :  0.044   0.170   1682
  Planarity :  0.005   0.052   1750
  Dihedral  :  6.134  58.746   1395
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.28 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.42 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.08 (0.18), residues: 1286
  helix: -3.73 (0.12), residues: 746
  sheet: -1.67 (0.89), residues: 36
  loop : -2.62 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 502 
 TYR   0.016   0.001   TYR B   9 
 PHE   0.021   0.001   PHE A 562 
 TRP   0.011   0.001   TRP B  63 
 HIS   0.006   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10402)
  covalent geometry    : angle       0.57729 (14112)
  hydrogen bonds       : bond        0.04687 (  308)
  hydrogen bonds       : angle       5.70057 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8335 (mp) cc_final: 0.7876 (tt)
REVERT: A  248 TYR cc_start: 0.7275 (t80) cc_final: 0.7071 (t80)
REVERT: A  293 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6161 (tt0)
REVERT: A  363 LEU cc_start: 0.8178 (mp) cc_final: 0.7827 (mp)
REVERT: A  612 GLN cc_start: 0.7528 (mt0) cc_final: 0.6764 (mt0)
REVERT: B   55 LEU cc_start: 0.8333 (mp) cc_final: 0.7875 (tt)
REVERT: B  248 TYR cc_start: 0.7244 (t80) cc_final: 0.7035 (t80)
REVERT: B  293 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6165 (tt0)
REVERT: B  363 LEU cc_start: 0.8180 (mp) cc_final: 0.7830 (mp)
REVERT: B  612 GLN cc_start: 0.7524 (mt0) cc_final: 0.6758 (mt0)
  outliers start: 19
  outliers final: 11
  residues processed: 139
  average time/residue: 0.0765
  time to fit residues: 16.5912
Evaluate side-chains
  127 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  337 GLN
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  337 GLN
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0370
   chunk 125 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0980
   chunk 34 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.9862

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
B  48 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.140641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.116426 restraints weight = 11784.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.115372 restraints weight = 16016.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.117460 restraints weight = 15800.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.117156 restraints weight = 10763.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.118137 restraints weight = 9364.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10402  Z= 0.111
  Angle     :  0.509   5.775  14112  Z= 0.272
  Chirality :  0.042   0.131   1682
  Planarity :  0.004   0.039   1750
  Dihedral  :  5.461  55.243   1391
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.65 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.05 (0.20), residues: 1286
  helix: -2.85 (0.16), residues: 760
  sheet: -1.37 (0.93), residues: 36
  loop : -2.22 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 569 
 TYR   0.014   0.001   TYR A   9 
 PHE   0.015   0.001   PHE B 130 
 TRP   0.008   0.001   TRP B  63 
 HIS   0.009   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10402)
  covalent geometry    : angle       0.50940 (14112)
  hydrogen bonds       : bond        0.03230 (  308)
  hydrogen bonds       : angle       4.80724 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A   69 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8281 (mp)
REVERT: A  248 TYR cc_start: 0.7316 (t80) cc_final: 0.7078 (t80)
REVERT: A  280 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.5730 (mp10)
REVERT: A  293 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6198 (tt0)
REVERT: A  363 LEU cc_start: 0.8204 (mp) cc_final: 0.7879 (mt)
REVERT: A  554 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7615 (mtm110)
REVERT: A  612 GLN cc_start: 0.7450 (mt0) cc_final: 0.6753 (mt0)
REVERT: A  715 ASP cc_start: 0.7846 (t0) cc_final: 0.7552 (t0)
REVERT: B   69 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8282 (mp)
REVERT: B  248 TYR cc_start: 0.7314 (t80) cc_final: 0.7060 (t80)
REVERT: B  280 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.5715 (mp10)
REVERT: B  293 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6202 (tt0)
REVERT: B  363 LEU cc_start: 0.8201 (mp) cc_final: 0.7876 (mt)
REVERT: B  554 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7614 (mtm110)
REVERT: B  612 GLN cc_start: 0.7450 (mt0) cc_final: 0.6752 (mt0)
REVERT: B  715 ASP cc_start: 0.7838 (t0) cc_final: 0.7540 (t0)
  outliers start: 18
  outliers final: 8
  residues processed: 131
  average time/residue: 0.0840
  time to fit residues: 16.2360
Evaluate side-chains
  131 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0020
   chunk 38 optimal weight:    0.8980
   chunk 115 optimal weight:    0.0370
   overall best weight:    0.5466

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
B   8 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.142444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.118178 restraints weight = 11850.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.117039 restraints weight = 15328.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.119142 restraints weight = 15194.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.118976 restraints weight = 10094.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.119850 restraints weight = 8976.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10402  Z= 0.085
  Angle     :  0.465   5.160  14112  Z= 0.248
  Chirality :  0.041   0.134   1682
  Planarity :  0.003   0.034   1750
  Dihedral  :  5.022  48.626   1391
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.73 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.21), residues: 1286
  helix: -2.34 (0.17), residues: 756
  sheet: -0.82 (1.02), residues: 36
  loop : -1.84 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 569 
 TYR   0.015   0.001   TYR B 545 
 PHE   0.013   0.001   PHE A 130 
 TRP   0.008   0.001   TRP B  63 
 HIS   0.003   0.000   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 (10402)
  covalent geometry    : angle       0.46518 (14112)
  hydrogen bonds       : bond        0.02557 (  308)
  hydrogen bonds       : angle       4.39624 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   69 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8319 (mp)
REVERT: A  248 TYR cc_start: 0.7382 (t80) cc_final: 0.7110 (t80)
REVERT: A  280 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5417 (mp10)
REVERT: A  363 LEU cc_start: 0.8260 (mp) cc_final: 0.7935 (mt)
REVERT: A  410 THR cc_start: 0.8930 (p) cc_final: 0.8723 (t)
REVERT: A  554 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7592 (mtm110)
REVERT: A  612 GLN cc_start: 0.7397 (mt0) cc_final: 0.6739 (mt0)
REVERT: A  715 ASP cc_start: 0.7748 (t0) cc_final: 0.7381 (t0)
REVERT: B   69 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8319 (mp)
REVERT: B  248 TYR cc_start: 0.7381 (t80) cc_final: 0.7109 (t80)
REVERT: B  280 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.5404 (mp10)
REVERT: B  363 LEU cc_start: 0.8255 (mp) cc_final: 0.7938 (mt)
REVERT: B  410 THR cc_start: 0.8928 (p) cc_final: 0.8721 (t)
REVERT: B  554 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7592 (mtm110)
REVERT: B  612 GLN cc_start: 0.7396 (mt0) cc_final: 0.6740 (mt0)
REVERT: B  715 ASP cc_start: 0.7740 (t0) cc_final: 0.7369 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 140
  average time/residue: 0.0856
  time to fit residues: 17.8050
Evaluate side-chains
  138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 123 optimal weight:    0.0970
   chunk 101 optimal weight:    7.9990
   chunk 113 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
B  48 GLN
B 454 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.138179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.113891 restraints weight = 11816.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.113029 restraints weight = 15406.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.114245 restraints weight = 16590.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.114377 restraints weight = 11551.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.116096 restraints weight = 10569.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10402  Z= 0.197
  Angle     :  0.566   5.347  14112  Z= 0.295
  Chirality :  0.044   0.133   1682
  Planarity :  0.004   0.033   1750
  Dihedral  :  5.260  42.571   1391
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.01 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.21), residues: 1286
  helix: -2.28 (0.17), residues: 756
  sheet: -1.41 (0.93), residues: 36
  loop : -1.90 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 569 
 TYR   0.025   0.002   TYR A   9 
 PHE   0.019   0.001   PHE B 130 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (10402)
  covalent geometry    : angle       0.56593 (14112)
  hydrogen bonds       : bond        0.03435 (  308)
  hydrogen bonds       : angle       4.51337 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.5844 (mp10)
REVERT: A  363 LEU cc_start: 0.8345 (mp) cc_final: 0.7994 (mt)
REVERT: A  404 GLU cc_start: 0.6713 (tt0) cc_final: 0.6505 (tt0)
REVERT: A  608 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6483 (pp)
REVERT: A  612 GLN cc_start: 0.7446 (mt0) cc_final: 0.6690 (mt0)
REVERT: B  280 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.5833 (mp10)
REVERT: B  363 LEU cc_start: 0.8341 (mp) cc_final: 0.7994 (mt)
REVERT: B  404 GLU cc_start: 0.6718 (tt0) cc_final: 0.6504 (tt0)
REVERT: B  608 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6482 (pp)
REVERT: B  612 GLN cc_start: 0.7447 (mt0) cc_final: 0.6690 (mt0)
  outliers start: 37
  outliers final: 30
  residues processed: 139
  average time/residue: 0.0832
  time to fit residues: 17.3113
Evaluate side-chains
  148 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain A residue  722 MET
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  661 VAL
Chi-restraints excluded: chain B residue  673 GLU
Chi-restraints excluded: chain B residue  712 THR
Chi-restraints excluded: chain B residue  722 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0670
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 106 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.3522

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.139506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.115211 restraints weight = 11874.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.114092 restraints weight = 16122.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.116508 restraints weight = 15236.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.115980 restraints weight = 10981.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.116824 restraints weight = 9216.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10402  Z= 0.121
  Angle     :  0.494   5.097  14112  Z= 0.263
  Chirality :  0.042   0.127   1682
  Planarity :  0.003   0.032   1750
  Dihedral  :  5.016  33.944   1391
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.71 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.22), residues: 1286
  helix: -1.99 (0.18), residues: 748
  sheet: -1.26 (0.95), residues: 36
  loop : -1.72 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  52 
 TYR   0.015   0.001   TYR A   9 
 PHE   0.014   0.001   PHE A 130 
 TRP   0.009   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10402)
  covalent geometry    : angle       0.49401 (14112)
  hydrogen bonds       : bond        0.02811 (  308)
  hydrogen bonds       : angle       4.35726 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 120
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.6772 (ptp90) cc_final: 0.6339 (ttp80)
REVERT: A  280 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.5820 (mp10)
REVERT: A  363 LEU cc_start: 0.8335 (mp) cc_final: 0.7989 (mt)
REVERT: A  404 GLU cc_start: 0.6558 (tt0) cc_final: 0.6338 (tt0)
REVERT: A  612 GLN cc_start: 0.7440 (mt0) cc_final: 0.6736 (mt0)
REVERT: B   52 ARG cc_start: 0.6781 (ptp90) cc_final: 0.6341 (ttp80)
REVERT: B  236 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.8151 (m)
REVERT: B  280 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.5821 (mp10)
REVERT: B  363 LEU cc_start: 0.8336 (mp) cc_final: 0.7993 (mt)
REVERT: B  404 GLU cc_start: 0.6559 (tt0) cc_final: 0.6330 (tt0)
REVERT: B  612 GLN cc_start: 0.7452 (mt0) cc_final: 0.6750 (mt0)
REVERT: B  715 ASP cc_start: 0.7835 (t0) cc_final: 0.7634 (t0)
  outliers start: 41
  outliers final: 30
  residues processed: 146
  average time/residue: 0.0741
  time to fit residues: 16.7880
Evaluate side-chains
  145 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  236 SER
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  320 ASP
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  640 GLU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  661 VAL
Chi-restraints excluded: chain B residue  673 GLU
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 65 optimal weight:    0.0020
   chunk 24 optimal weight:    8.9990
   chunk 93 optimal weight:    5.9990
   chunk 79 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    0.1980
   chunk 8 optimal weight:    0.2980
   chunk 112 optimal weight:    0.0010
   overall best weight:    0.2194

-------------------------------------------------------------------------------
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 = 0.3465 r_free = 0.3465 target = 0.143759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.119982 restraints weight = 11633.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.119632 restraints weight = 12275.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.120408 restraints weight = 11736.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.120748 restraints weight = 10025.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.121318 restraints weight = 8649.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10402  Z= 0.078
  Angle     :  0.449   5.200  14112  Z= 0.241
  Chirality :  0.040   0.129   1682
  Planarity :  0.003   0.035   1750
  Dihedral  :  4.483  18.533   1391
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.78 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.23), residues: 1286
  helix: -1.55 (0.19), residues: 760
  sheet: -0.59 (1.07), residues: 36
  loop : -1.45 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  52 
 TYR   0.009   0.001   TYR A 104 
 PHE   0.010   0.001   PHE B 562 
 TRP   0.012   0.001   TRP B  63 
 HIS   0.003   0.000   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00162 (10402)
  covalent geometry    : angle       0.44854 (14112)
  hydrogen bonds       : bond        0.02119 (  308)
  hydrogen bonds       : angle       4.01626 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.6830 (tp40) cc_final: 0.6630 (tp-100)
REVERT: A   52 ARG cc_start: 0.6660 (ptp90) cc_final: 0.6215 (ttp80)
REVERT: A  280 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.5447 (mp10)
REVERT: A  363 LEU cc_start: 0.8228 (mp) cc_final: 0.7872 (mt)
REVERT: A  612 GLN cc_start: 0.7470 (mt0) cc_final: 0.6821 (mt0)
REVERT: B   48 GLN cc_start: 0.6856 (tp40) cc_final: 0.6653 (tp-100)
REVERT: B   52 ARG cc_start: 0.6663 (ptp90) cc_final: 0.6210 (ttp80)
REVERT: B  280 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.5449 (mp10)
REVERT: B  363 LEU cc_start: 0.8225 (mp) cc_final: 0.7872 (mt)
REVERT: B  612 GLN cc_start: 0.7470 (mt0) cc_final: 0.6823 (mt0)
REVERT: B  715 ASP cc_start: 0.7632 (t0) cc_final: 0.7229 (t0)
  outliers start: 25
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0750
  time to fit residues: 14.6657
Evaluate side-chains
  133 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  320 ASP
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  640 GLU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  661 VAL
Chi-restraints excluded: chain B residue  673 GLU
Chi-restraints excluded: chain B residue  712 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 129 optimal weight:    0.7980
   chunk 96 optimal weight:    5.9990
   chunk 93 optimal weight:    0.2980
   chunk 119 optimal weight:    9.9990
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0170
   chunk 84 optimal weight:    0.0970
   chunk 102 optimal weight:    7.9990
   overall best weight:    0.8418

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.142508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.118076 restraints weight = 11693.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.116856 restraints weight = 16520.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.118166 restraints weight = 17226.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.118376 restraints weight = 11621.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.118694 restraints weight = 10765.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10402  Z= 0.092
  Angle     :  0.454   5.148  14112  Z= 0.242
  Chirality :  0.041   0.127   1682
  Planarity :  0.003   0.036   1750
  Dihedral  :  4.424  17.551   1390
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.25 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.23), residues: 1286
  helix: -1.46 (0.19), residues: 764
  sheet: -0.61 (1.05), residues: 36
  loop : -1.37 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 197 
 TYR   0.012   0.001   TYR B   9 
 PHE   0.013   0.001   PHE B 130 
 TRP   0.008   0.001   TRP B  63 
 HIS   0.002   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (10402)
  covalent geometry    : angle       0.45431 (14112)
  hydrogen bonds       : bond        0.02323 (  308)
  hydrogen bonds       : angle       4.00066 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.6767 (tp40) cc_final: 0.6544 (tp-100)
REVERT: A   52 ARG cc_start: 0.6672 (ptp90) cc_final: 0.6205 (ttp80)
REVERT: A  280 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.5505 (mp10)
REVERT: A  363 LEU cc_start: 0.8266 (mp) cc_final: 0.7926 (mt)
REVERT: A  612 GLN cc_start: 0.7470 (mt0) cc_final: 0.6819 (mt0)
REVERT: B   48 GLN cc_start: 0.6809 (tp40) cc_final: 0.6588 (tp-100)
REVERT: B   52 ARG cc_start: 0.6677 (ptp90) cc_final: 0.6205 (ttp80)
REVERT: B  280 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.5488 (mp10)
REVERT: B  363 LEU cc_start: 0.8266 (mp) cc_final: 0.7924 (mt)
REVERT: B  612 GLN cc_start: 0.7469 (mt0) cc_final: 0.6818 (mt0)
REVERT: B  715 ASP cc_start: 0.7745 (t0) cc_final: 0.7376 (t0)
  outliers start: 32
  outliers final: 28
  residues processed: 133
  average time/residue: 0.0775
  time to fit residues: 15.7695
Evaluate side-chains
  137 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain A residue  722 MET
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  320 ASP
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  405 SER
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  640 GLU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  661 VAL
Chi-restraints excluded: chain B residue  673 GLU
Chi-restraints excluded: chain B residue  712 THR
Chi-restraints excluded: chain B residue  722 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 91 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.143117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.119167 restraints weight = 11621.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.118886 restraints weight = 12284.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.119405 restraints weight = 11750.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.119650 restraints weight = 10189.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.122058 restraints weight = 8963.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10402  Z= 0.089
  Angle     :  0.454   5.152  14112  Z= 0.242
  Chirality :  0.041   0.126   1682
  Planarity :  0.003   0.036   1750
  Dihedral  :  4.387  17.131   1390
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.89 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.23), residues: 1286
  helix: -1.35 (0.19), residues: 764
  sheet: -0.70 (1.04), residues: 36
  loop : -1.32 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 312 
 TYR   0.015   0.001   TYR B 361 
 PHE   0.012   0.001   PHE B 130 
 TRP   0.009   0.001   TRP A  63 
 HIS   0.002   0.000   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 (10402)
  covalent geometry    : angle       0.45390 (14112)
  hydrogen bonds       : bond        0.02311 (  308)
  hydrogen bonds       : angle       4.00431 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.6812 (tp40) cc_final: 0.6588 (tp-100)
REVERT: A   52 ARG cc_start: 0.6609 (ptp90) cc_final: 0.6151 (ttp80)
REVERT: A  280 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.5494 (mp10)
REVERT: A  363 LEU cc_start: 0.8187 (mp) cc_final: 0.7832 (mt)
REVERT: A  612 GLN cc_start: 0.7437 (mt0) cc_final: 0.6797 (mt0)
REVERT: B   48 GLN cc_start: 0.6845 (tp40) cc_final: 0.6631 (tp-100)
REVERT: B   52 ARG cc_start: 0.6612 (ptp90) cc_final: 0.6143 (ttp80)
REVERT: B  280 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.5486 (mp10)
REVERT: B  363 LEU cc_start: 0.8187 (mp) cc_final: 0.7837 (mt)
REVERT: B  612 GLN cc_start: 0.7438 (mt0) cc_final: 0.6800 (mt0)
REVERT: B  715 ASP cc_start: 0.7699 (t0) cc_final: 0.7289 (t0)
  outliers start: 35
  outliers final: 29
  residues processed: 131
  average time/residue: 0.0739
  time to fit residues: 15.0262
Evaluate side-chains
  134 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain A residue  722 MET
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  320 ASP
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  640 GLU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  661 VAL
Chi-restraints excluded: chain B residue  673 GLU
Chi-restraints excluded: chain B residue  712 THR
Chi-restraints excluded: chain B residue  722 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.142585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.117895 restraints weight = 11573.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.117814 restraints weight = 12012.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.119143 restraints weight = 11856.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.119378 restraints weight = 8218.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.119543 restraints weight = 7945.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10402  Z= 0.097
  Angle     :  0.460   5.145  14112  Z= 0.244
  Chirality :  0.041   0.130   1682
  Planarity :  0.003   0.035   1750
  Dihedral  :  4.351  16.602   1390
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.25 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.23), residues: 1286
  helix: -1.22 (0.19), residues: 774
  sheet: -0.72 (1.03), residues: 36
  loop : -1.36 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 312 
 TYR   0.012   0.001   TYR B   9 
 PHE   0.013   0.001   PHE B 130 
 TRP   0.008   0.001   TRP B  63 
 HIS   0.001   0.000   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10402)
  covalent geometry    : angle       0.45963 (14112)
  hydrogen bonds       : bond        0.02405 (  308)
  hydrogen bonds       : angle       4.01753 (  876)

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

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

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2572 Ramachandran restraints generated.
    1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 105
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.6846 (tp40) cc_final: 0.6634 (tp-100)
REVERT: A   52 ARG cc_start: 0.6620 (ptp90) cc_final: 0.6163 (ttp80)
REVERT: A  280 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.5474 (mp10)
REVERT: A  363 LEU cc_start: 0.8183 (mp) cc_final: 0.7806 (mt)
REVERT: A  612 GLN cc_start: 0.7436 (mt0) cc_final: 0.6783 (mt0)
REVERT: B   48 GLN cc_start: 0.6812 (tp40) cc_final: 0.6603 (tp-100)
REVERT: B   52 ARG cc_start: 0.6624 (ptp90) cc_final: 0.6164 (ttp80)
REVERT: B  280 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.5477 (mp10)
REVERT: B  363 LEU cc_start: 0.8185 (mp) cc_final: 0.7813 (mt)
REVERT: B  612 GLN cc_start: 0.7434 (mt0) cc_final: 0.6754 (mt0)
REVERT: B  715 ASP cc_start: 0.7747 (t0) cc_final: 0.7349 (t0)
  outliers start: 35
  outliers final: 31
  residues processed: 127
  average time/residue: 0.0759
  time to fit residues: 14.7855
Evaluate side-chains
  138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  280 GLN
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  640 GLU
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  673 GLU
Chi-restraints excluded: chain A residue  712 THR
Chi-restraints excluded: chain A residue  722 MET
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  320 ASP
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  640 GLU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  661 VAL
Chi-restraints excluded: chain B residue  673 GLU
Chi-restraints excluded: chain B residue  712 THR
Chi-restraints excluded: chain B residue  722 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 89 optimal weight:    9.9990
   chunk 38 optimal weight:    0.0270
   chunk 16 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0470
   chunk 108 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 86 optimal weight:    0.2980
   chunk 111 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.144644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.121554 restraints weight = 11584.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.120874 restraints weight = 15772.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.122491 restraints weight = 13470.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.122497 restraints weight = 10194.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.124369 restraints weight = 8781.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10402  Z= 0.076
  Angle     :  0.435   5.260  14112  Z= 0.233
  Chirality :  0.040   0.130   1682
  Planarity :  0.003   0.036   1750
  Dihedral  :  4.163  16.470   1390
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.69 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.23), residues: 1286
  helix: -0.98 (0.19), residues: 776
  sheet: -0.57 (1.05), residues: 36
  loop : -1.29 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 460 
 TYR   0.011   0.001   TYR B 545 
 PHE   0.011   0.001   PHE B 130 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.001   0.000   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 (10402)
  covalent geometry    : angle       0.43490 (14112)
  hydrogen bonds       : bond        0.02074 (  308)
  hydrogen bonds       : angle       3.91070 (  876)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1464.20 seconds
wall clock time: 26 minutes 0.87 seconds (1560.87 seconds total)