Starting phenix.real_space_refine
on Sat Aug 23 01:43:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hf7_34715/08_2025/8hf7_34715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hf7_34715/08_2025/8hf7_34715.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hf7_34715/08_2025/8hf7_34715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hf7_34715/08_2025/8hf7_34715.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hf7_34715/08_2025/8hf7_34715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hf7_34715/08_2025/8hf7_34715.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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      28      5.16       5
     C    5784      2.51       5
     N    1478      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8978
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4424
          Classifications: {'peptide': 563}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 4424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4424
          Classifications: {'peptide': 563}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 65
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'UNK:plan-1': 13}
          Unresolved non-hydrogen planarities: 13
    Chain: "C"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 65
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'UNK:plan-1': 13}
          Unresolved non-hydrogen planarities: 13
  Time building chain proxies: 2.22, per 1000 atoms: 0.25
  Number of scatterers: 8978
  At special positions: 0
  Unit cell: (80.652, 81.51, 140.712, 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      28     16.00
     O    1688      8.00
     N    1478      7.00
     C    5784      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: 0.82
  Conformation dependent library (CDL) restraints added in 244.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2176

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 7 sheets defined
      63.6% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 4.082A  pdb=" N   VAL A 162 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 158 through 163'
    Processing helix  chain 'A' and resid 167 through 188
      removed outlier: 3.749A  pdb=" N   VAL A 178 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR A 179 " --> pdb=" O   THR A 175 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN A 182 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 250
      removed outlier: 4.358A  pdb=" N   ILE A 239 " --> pdb=" O   GLN A 235 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   ASP A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   VAL A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   HIS A 248 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE A 250 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 3.902A  pdb=" N   PHE A 257 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 272
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 304
      removed outlier: 3.836A  pdb=" N   THR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   VAL A 290 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   SER A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A 298 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   VAL A 299 " --> pdb=" O   ILE A 295 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 312
    Processing helix  chain 'A' and resid 313 through 325
      removed outlier: 4.013A  pdb=" N   ILE A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TYR A 318 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 353
      removed outlier: 4.426A  pdb=" N   GLU A 330 " --> pdb=" O   MET A 326 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   ARG A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ASP A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ASN A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 3.769A  pdb=" N   ILE A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   SER A 359 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 416
      removed outlier: 4.446A  pdb=" N   LYS A 369 " --> pdb=" O   GLN A 365 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 444
      removed outlier: 4.376A  pdb=" N   VAL A 432 " --> pdb=" O   ASN A 428 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   TYR A 433 " --> pdb=" O   THR A 429 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
    Processing helix  chain 'A' and resid 444 through 459
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 528 through 532
      removed outlier: 3.622A  pdb=" N   VAL A 531 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN A 532 " --> pdb=" O   MET A 529 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 528 through 532'
    Processing helix  chain 'A' and resid 553 through 558
      removed outlier: 4.235A  pdb=" N   GLN A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 579
      removed outlier: 3.728A  pdb=" N   ASN A 577 " --> pdb=" O   THR A 573 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU A 579 " --> pdb=" O   LEU A 575 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 573 through 579'
    Processing helix  chain 'A' and resid 587 through 596
      removed outlier: 3.655A  pdb=" N   ILE A 591 " --> pdb=" O   THR A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 634
      removed outlier: 3.707A  pdb=" N   ILE A 630 " --> pdb=" O   GLN A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 665
      removed outlier: 3.631A  pdb=" N   ILE A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 682
      removed outlier: 3.865A  pdb=" N   GLU A 682 " --> pdb=" O   THR A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 708
      removed outlier: 3.939A  pdb=" N   GLN A 707 " --> pdb=" O   LEU A 704 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLY A 708 " --> pdb=" O   LEU A 705 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 704 through 708'
    Processing helix  chain 'A' and resid 710 through 717
      removed outlier: 3.529A  pdb=" N   LEU A 714 " --> pdb=" O   PHE A 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 163
      removed outlier: 4.042A  pdb=" N   VAL B 162 " --> pdb=" O   ILE B 158 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LYS B 163 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 158 through 163'
    Processing helix  chain 'B' and resid 167 through 183
      removed outlier: 3.560A  pdb=" N   LEU B 173 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA B 174 " --> pdb=" O   ASN B 170 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   VAL B 178 " --> pdb=" O   ALA B 174 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR B 179 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'B' and resid 202 through 250
      removed outlier: 4.478A  pdb=" N   ILE B 239 " --> pdb=" O   GLN B 235 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   ASP B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   VAL B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   HIS B 248 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   PHE B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 260
      removed outlier: 3.829A  pdb=" N   PHE B 257 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 272
    Processing helix  chain 'B' and resid 275 through 277
      No H-bonds generated for 'chain 'B' and resid 275 through 277'
    Processing helix  chain 'B' and resid 278 through 304
      removed outlier: 3.820A  pdb=" N   THR B 282 " --> pdb=" O   ALA B 278 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   VAL B 290 " --> pdb=" O   ILE B 286 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   SER B 291 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU B 298 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   VAL B 299 " --> pdb=" O   ILE B 295 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASN B 304 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 312
    Processing helix  chain 'B' and resid 313 through 325
      removed outlier: 4.036A  pdb=" N   ILE B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR B 318 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 353
      removed outlier: 4.131A  pdb=" N   GLU B 330 " --> pdb=" O   MET B 326 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ARG B 334 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ASP B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASN B 340 " --> pdb=" O   THR B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 361
      removed outlier: 3.721A  pdb=" N   ILE B 357 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   SER B 359 " --> pdb=" O   GLU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 416
      removed outlier: 4.469A  pdb=" N   LYS B 369 " --> pdb=" O   GLN B 365 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASP B 416 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 444
      removed outlier: 4.391A  pdb=" N   VAL B 432 " --> pdb=" O   ASN B 428 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   TYR B 433 " --> pdb=" O   THR B 429 " (cutoff:3.500A)
      Proline residue:  B 437  - end of helix
    Processing helix  chain 'B' and resid 444 through 459
    Processing helix  chain 'B' and resid 459 through 464
      removed outlier: 3.874A  pdb=" N   VAL B 464 " --> pdb=" O   GLU B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 527
    Processing helix  chain 'B' and resid 528 through 532
      removed outlier: 3.889A  pdb=" N   VAL B 531 " --> pdb=" O   LYS B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 558
      removed outlier: 4.228A  pdb=" N   GLN B 558 " --> pdb=" O   LYS B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 579
      removed outlier: 3.514A  pdb=" N   LEU B 578 " --> pdb=" O   ILE B 574 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU B 579 " --> pdb=" O   LEU B 575 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 574 through 579'
    Processing helix  chain 'B' and resid 587 through 596
      removed outlier: 3.741A  pdb=" N   ILE B 591 " --> pdb=" O   THR B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 634
      removed outlier: 3.602A  pdb=" N   ILE B 630 " --> pdb=" O   GLN B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 665
      removed outlier: 3.586A  pdb=" N   ARG B 659 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 665 " --> pdb=" O   VAL B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 682
      removed outlier: 3.857A  pdb=" N   GLU B 682 " --> pdb=" O   THR B 679 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 704 through 708
      removed outlier: 3.927A  pdb=" N   GLN B 707 " --> pdb=" O   LEU B 704 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLY B 708 " --> pdb=" O   LEU B 705 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 704 through 708'
    Processing helix  chain 'B' and resid 710 through 717
      removed outlier: 3.529A  pdb=" N   LEU B 714 " --> pdb=" O   PHE B 710 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503
      removed outlier: 5.706A  pdb=" N   VAL A 489 " --> pdb=" O   ASP A 502 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   PHE A 486 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   SER A 542 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   GLN A 488 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   GLU A 540 " --> pdb=" O   GLN A 488 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 671 through 674
      removed outlier: 3.720A  pdb=" N   PHE A 673 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LYS A 512 " --> pdb=" O   LYS A 686 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL A 688 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ALA A 514 " --> pdb=" O   VAL A 688 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   LEU A 690 " --> pdb=" O   ALA A 514 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   VAL A 687 " --> pdb=" O   GLU A 698 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   GLU A 698 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A 696 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 562
    Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 503
      removed outlier: 5.705A  pdb=" N   VAL B 489 " --> pdb=" O   ASP B 502 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   PHE B 486 " --> pdb=" O   SER B 542 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   SER B 542 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   GLN B 488 " --> pdb=" O   GLU B 540 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   GLU B 540 " --> pdb=" O   GLN B 488 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 671 through 674
      removed outlier: 3.784A  pdb=" N   PHE B 673 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   LYS B 512 " --> pdb=" O   LYS B 686 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL B 688 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ALA B 514 " --> pdb=" O   VAL B 688 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   LEU B 690 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   VAL B 687 " --> pdb=" O   GLU B 698 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   GLU B 698 " --> pdb=" O   VAL B 687 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL B 689 " --> pdb=" O   VAL B 696 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL B 696 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 560 through 562
    Processing sheet with id=AA7, first strand: chain 'B' and resid 572 through 573
      removed outlier: 3.844A  pdb=" N   GLY B 572 " --> pdb=" O   THR B 616 " (cutoff:3.500A)

    457 hydrogen bonds defined for protein.
    1338 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: 1.13

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1536
        1.32 -     1.45: 2192
        1.45 -     1.57: 5322
        1.57 -     1.69: 0
        1.69 -     1.82: 56
  Bond restraints: 9106
  Sorted by residual:
  bond pdb=" CA  UNK D   4 "
       pdb=" C   UNK D   4 "
    ideal  model  delta    sigma   weight residual
    1.525  1.433  0.092 2.10e-02 2.27e+03 1.92e+01
  bond pdb=" CA  GLN B 612 "
       pdb=" C   GLN B 612 "
    ideal  model  delta    sigma   weight residual
    1.531  1.482  0.049 1.12e-02 7.97e+03 1.89e+01
  bond pdb=" CA  UNK D  10 "
       pdb=" C   UNK D  10 "
    ideal  model  delta    sigma   weight residual
    1.525  1.435  0.090 2.10e-02 2.27e+03 1.84e+01
  bond pdb=" CA  THR B 613 "
       pdb=" C   THR B 613 "
    ideal  model  delta    sigma   weight residual
    1.522  1.473  0.049 1.31e-02 5.83e+03 1.38e+01
  bond pdb=" CA  UNK C  10 "
       pdb=" C   UNK C  10 "
    ideal  model  delta    sigma   weight residual
    1.525  1.452  0.073 2.10e-02 2.27e+03 1.21e+01
  ... (remaining 9101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 11643
        2.51 -     5.03: 520
        5.03 -     7.54: 112
        7.54 -    10.05: 52
       10.05 -    12.57: 15
  Bond angle restraints: 12342
  Sorted by residual:
  angle pdb=" N   ASN B 610 "
        pdb=" CA  ASN B 610 "
        pdb=" C   ASN B 610 "
      ideal   model   delta    sigma   weight residual
     111.87  101.49   10.38 1.41e+00 5.03e-01 5.42e+01
  angle pdb=" N   MET A 607 "
        pdb=" CA  MET A 607 "
        pdb=" C   MET A 607 "
      ideal   model   delta    sigma   weight residual
     109.24   99.38    9.86 1.39e+00 5.18e-01 5.03e+01
  angle pdb=" C   UNK D  12 "
        pdb=" CA  UNK D  12 "
        pdb=" CB  UNK D  12 "
      ideal   model   delta    sigma   weight residual
     110.08  121.43  -11.35 1.90e+00 2.77e-01 3.57e+01
  angle pdb=" C   SER B 501 "
        pdb=" N   ASP B 502 "
        pdb=" CA  ASP B 502 "
      ideal   model   delta    sigma   weight residual
     122.46  129.65   -7.19 1.41e+00 5.03e-01 2.60e+01
  angle pdb=" C   SER A 501 "
        pdb=" N   ASP A 502 "
        pdb=" CA  ASP A 502 "
      ideal   model   delta    sigma   weight residual
     122.46  129.62   -7.16 1.41e+00 5.03e-01 2.58e+01
  ... (remaining 12337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 4991
       17.72 -    35.43: 436
       35.43 -    53.15: 74
       53.15 -    70.86: 15
       70.86 -    88.58: 6
  Dihedral angle restraints: 5522
    sinusoidal: 2152
      harmonic: 3370
  Sorted by residual:
  dihedral pdb=" C   UNK D  12 "
           pdb=" N   UNK D  12 "
           pdb=" CA  UNK D  12 "
           pdb=" CB  UNK D  12 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.73   17.13     0      2.50e+00 1.60e-01 4.69e+01
  dihedral pdb=" N   UNK D  12 "
           pdb=" C   UNK D  12 "
           pdb=" CA  UNK D  12 "
           pdb=" CB  UNK D  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.07  -14.27     0      2.50e+00 1.60e-01 3.26e+01
  dihedral pdb=" CA  THR B 195 "
           pdb=" C   THR B 195 "
           pdb=" N   TYR B 196 "
           pdb=" CA  TYR B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.96  -28.04     0      5.00e+00 4.00e-02 3.14e+01
  ... (remaining 5519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 1406
       0.122 -    0.244: 94
       0.244 -    0.366: 11
       0.366 -    0.489: 2
       0.489 -    0.611: 1
  Chirality restraints: 1514
  Sorted by residual:
  chirality pdb=" CA  UNK D  12 "
            pdb=" N   UNK D  12 "
            pdb=" C   UNK D  12 "
            pdb=" CB  UNK D  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.52    1.91    0.61 2.00e-01 2.50e+01 9.33e+00
  chirality pdb=" CB  VAL A 414 "
            pdb=" CA  VAL A 414 "
            pdb=" CG1 VAL A 414 "
            pdb=" CG2 VAL A 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.40 2.00e-01 2.50e+01 4.09e+00
  chirality pdb=" CB  VAL B 414 "
            pdb=" CA  VAL B 414 "
            pdb=" CG1 VAL B 414 "
            pdb=" CG2 VAL B 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.24   -0.39 2.00e-01 2.50e+01 3.72e+00
  ... (remaining 1511 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 166 "    0.019 2.00e-02 2.50e+03   3.62e-02 1.31e+01
        pdb=" C   GLY A 166 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   GLY A 166 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU A 167 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 197 "    0.056 5.00e-02 4.00e+02   8.66e-02 1.20e+01
        pdb=" N   PRO A 198 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 198 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 198 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  UNK D   5 "    0.015 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   UNK D   5 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   UNK D   5 "    0.021 2.00e-02 2.50e+03
        pdb=" N   UNK D   6 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 2573
        2.82 -     3.34: 8523
        3.34 -     3.86: 14897
        3.86 -     4.38: 15743
        4.38 -     4.90: 26484
  Nonbonded interactions: 68220
  Sorted by model distance:
  nonbonded pdb=" CB  ASN B 561 "
            pdb=" CD2 LEU B 643 "
     model   vdw
     2.294 3.860
  nonbonded pdb=" CB  ASN A 561 "
            pdb=" CD2 LEU A 643 "
     model   vdw
     2.309 3.860
  nonbonded pdb=" O   LEU A 279 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   LEU B 279 "
            pdb=" OG1 THR B 282 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OG  SER A 519 "
            pdb=" O   SER B 651 "
     model   vdw
     2.331 3.040
  ... (remaining 68215 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.460
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
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   0.092   9106  Z= 0.340
  Angle     :  1.342  12.566  12342  Z= 0.674
  Chirality :  0.069   0.611   1514
  Planarity :  0.007   0.087   1544
  Dihedral  : 14.022  88.580   3346
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  :  5.88 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  1.92 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.03 (0.21), residues: 1122
  helix: -1.77 (0.17), residues: 634
  sheet: -1.21 (0.59), residues: 48
  loop : -2.28 (0.25), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 629 
 TYR   0.023   0.002   TYR A 559 
 PHE   0.041   0.002   PHE A 257 
 TRP   0.003   0.001   TRP A 408 
 HIS   0.002   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 9106)
  covalent geometry    : angle       1.34201 (12342)
  hydrogen bonds       : bond        0.14547 (  457)
  hydrogen bonds       : angle       5.60355 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 172
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  192 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (mp)
REVERT: A  563 LEU cc_start: 0.8801 (tp) cc_final: 0.8442 (tt)
REVERT: A  662 ASP cc_start: 0.9026 (m-30) cc_final: 0.8657 (m-30)
REVERT: B  431 LEU cc_start: 0.8845 (tp) cc_final: 0.8636 (mt)
REVERT: B  529 MET cc_start: 0.9375 (pmm) cc_final: 0.9061 (pmm)
REVERT: B  563 LEU cc_start: 0.8368 (tt) cc_final: 0.8112 (tt)
  outliers start: 6
  outliers final: 3
  residues processed: 177
  average time/residue: 0.0619
  time to fit residues: 16.5610
Evaluate side-chains
  126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  613 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   40.0000
   chunk 49 optimal weight:   30.0000
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    0.4980
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 273 ASN
A 445 GLN
B 273 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.105928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.082118 restraints weight = 38954.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.084469 restraints weight = 22332.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.085953 restraints weight = 15231.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.086906 restraints weight = 11753.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.087509 restraints weight = 9941.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9106  Z= 0.157
  Angle     :  0.736   9.320  12342  Z= 0.367
  Chirality :  0.043   0.227   1514
  Planarity :  0.004   0.037   1544
  Dihedral  :  5.839  46.917   1242
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.90 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.34 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.24), residues: 1122
  helix:  0.10 (0.21), residues: 644
  sheet: -1.03 (0.75), residues: 34
  loop : -1.98 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 593 
 TYR   0.024   0.002   TYR B 188 
 PHE   0.016   0.001   PHE B 257 
 TRP   0.003   0.001   TRP B 408 
 HIS   0.002   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9106)
  covalent geometry    : angle       0.73562 (12342)
  hydrogen bonds       : bond        0.06311 (  457)
  hydrogen bonds       : angle       4.21625 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8974 (mm)
REVERT: A  529 MET cc_start: 0.9568 (pmm) cc_final: 0.9197 (pmm)
REVERT: A  561 ASN cc_start: 0.8688 (t0) cc_final: 0.8109 (t0)
REVERT: B  300 LEU cc_start: 0.9143 (mm) cc_final: 0.8924 (mm)
REVERT: B  529 MET cc_start: 0.9439 (pmm) cc_final: 0.9085 (pmm)
  outliers start: 23
  outliers final: 14
  residues processed: 152
  average time/residue: 0.0598
  time to fit residues: 14.0823
Evaluate side-chains
  134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  490 HIS
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  662 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 84 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 105 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 490 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.103484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.080665 restraints weight = 38932.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.082914 restraints weight = 22018.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.084329 restraints weight = 14882.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.085268 restraints weight = 11460.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.085840 restraints weight = 9665.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9106  Z= 0.158
  Angle     :  0.718  12.696  12342  Z= 0.354
  Chirality :  0.043   0.201   1514
  Planarity :  0.004   0.032   1544
  Dihedral  :  5.210  47.350   1238
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.50 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.25), residues: 1122
  helix:  0.67 (0.21), residues: 640
  sheet: -1.13 (0.77), residues: 34
  loop : -1.74 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 593 
 TYR   0.031   0.002   TYR B 188 
 PHE   0.013   0.001   PHE A 257 
 TRP   0.003   0.001   TRP B 408 
 HIS   0.002   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9106)
  covalent geometry    : angle       0.71801 (12342)
  hydrogen bonds       : bond        0.06411 (  457)
  hydrogen bonds       : angle       4.26635 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9018 (mm)
REVERT: A  409 MET cc_start: 0.7942 (tpp) cc_final: 0.7681 (tpt)
REVERT: A  561 ASN cc_start: 0.8850 (t0) cc_final: 0.8237 (t0)
REVERT: B  300 LEU cc_start: 0.9245 (mm) cc_final: 0.9020 (mm)
REVERT: B  529 MET cc_start: 0.9436 (pmm) cc_final: 0.9061 (pmm)
  outliers start: 27
  outliers final: 21
  residues processed: 142
  average time/residue: 0.0616
  time to fit residues: 13.7680
Evaluate side-chains
  135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  490 HIS
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  560 ILE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  644 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  662 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 93 optimal weight:    0.3980
   chunk 16 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.4786

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.103421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.080510 restraints weight = 39855.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.082834 restraints weight = 22306.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.084324 restraints weight = 14886.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.085262 restraints weight = 11321.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.085829 restraints weight = 9524.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9106  Z= 0.141
  Angle     :  0.681  12.585  12342  Z= 0.333
  Chirality :  0.042   0.193   1514
  Planarity :  0.003   0.030   1544
  Dihedral  :  5.056  47.686   1238
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.53 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.42 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.25), residues: 1122
  helix:  0.94 (0.22), residues: 632
  sheet: -1.21 (0.78), residues: 34
  loop : -1.49 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 593 
 TYR   0.029   0.002   TYR B 559 
 PHE   0.010   0.001   PHE B 257 
 TRP   0.004   0.002   TRP B 408 
 HIS   0.002   0.001   HIS B 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9106)
  covalent geometry    : angle       0.68112 (12342)
  hydrogen bonds       : bond        0.06219 (  457)
  hydrogen bonds       : angle       4.20716 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4591 (t80) cc_final: 0.3921 (m-80)
REVERT: A  300 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9096 (mm)
REVERT: A  409 MET cc_start: 0.7929 (tpp) cc_final: 0.7590 (tpt)
REVERT: A  561 ASN cc_start: 0.8935 (t0) cc_final: 0.8316 (t0)
REVERT: A  662 ASP cc_start: 0.9154 (m-30) cc_final: 0.8753 (p0)
REVERT: B  300 LEU cc_start: 0.9309 (mm) cc_final: 0.9068 (mm)
REVERT: B  529 MET cc_start: 0.9443 (pmm) cc_final: 0.9151 (pmm)
  outliers start: 37
  outliers final: 26
  residues processed: 152
  average time/residue: 0.0552
  time to fit residues: 13.2533
Evaluate side-chains
  139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 ASN
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  179 THR
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  490 HIS
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  644 ILE
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  644 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 68 optimal weight:    8.9990
   chunk 108 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.105241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.082459 restraints weight = 39631.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.084810 restraints weight = 22362.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.086273 restraints weight = 14975.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.087224 restraints weight = 11457.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.087806 restraints weight = 9633.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9106  Z= 0.122
  Angle     :  0.693  12.687  12342  Z= 0.326
  Chirality :  0.041   0.183   1514
  Planarity :  0.003   0.032   1544
  Dihedral  :  4.871  47.930   1238
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.44 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 21.56 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.25), residues: 1122
  helix:  1.14 (0.21), residues: 640
  sheet: -1.21 (0.78), residues: 34
  loop : -1.64 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 593 
 TYR   0.026   0.001   TYR B 559 
 PHE   0.010   0.001   PHE B 257 
 TRP   0.005   0.001   TRP B 408 
 HIS   0.002   0.000   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9106)
  covalent geometry    : angle       0.69309 (12342)
  hydrogen bonds       : bond        0.05700 (  457)
  hydrogen bonds       : angle       4.08567 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4444 (t80) cc_final: 0.3721 (m-80)
REVERT: A  300 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9093 (mm)
REVERT: A  409 MET cc_start: 0.7974 (tpp) cc_final: 0.7735 (tpt)
REVERT: A  561 ASN cc_start: 0.8844 (t0) cc_final: 0.8267 (t0)
REVERT: A  607 MET cc_start: 0.8663 (ppp) cc_final: 0.8423 (ppp)
REVERT: A  662 ASP cc_start: 0.9137 (m-30) cc_final: 0.8756 (p0)
REVERT: B  300 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9110 (mm)
  outliers start: 29
  outliers final: 22
  residues processed: 149
  average time/residue: 0.0596
  time to fit residues: 13.9347
Evaluate side-chains
  130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  644 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0970
   chunk 97 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 76 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    2.7184

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.102852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.079449 restraints weight = 39656.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.081695 restraints weight = 22928.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.083104 restraints weight = 15616.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.084056 restraints weight = 12059.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.084631 restraints weight = 10179.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9106  Z= 0.147
  Angle     :  0.710  12.651  12342  Z= 0.344
  Chirality :  0.043   0.195   1514
  Planarity :  0.003   0.033   1544
  Dihedral  :  4.947  48.084   1238
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.53 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 22.77 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.25), residues: 1122
  helix:  1.20 (0.22), residues: 630
  sheet: -1.24 (0.80), residues: 34
  loop : -1.47 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 593 
 TYR   0.040   0.002   TYR B 188 
 PHE   0.010   0.001   PHE B 256 
 TRP   0.004   0.001   TRP B 408 
 HIS   0.002   0.001   HIS B 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9106)
  covalent geometry    : angle       0.70963 (12342)
  hydrogen bonds       : bond        0.06064 (  457)
  hydrogen bonds       : angle       4.23120 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  187 TYR cc_start: 0.4640 (t80) cc_final: 0.3952 (m-80)
REVERT: A  409 MET cc_start: 0.8010 (tpp) cc_final: 0.7723 (tpt)
REVERT: A  561 ASN cc_start: 0.8904 (t0) cc_final: 0.8331 (t0)
REVERT: A  607 MET cc_start: 0.8662 (ppp) cc_final: 0.8451 (ppp)
REVERT: A  662 ASP cc_start: 0.9155 (m-30) cc_final: 0.8772 (p0)
REVERT: A  679 THR cc_start: 0.6455 (OUTLIER) cc_final: 0.6151 (t)
REVERT: B  300 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9096 (mm)
REVERT: B  561 ASN cc_start: 0.9092 (t0) cc_final: 0.8445 (t0)
  outliers start: 41
  outliers final: 29
  residues processed: 144
  average time/residue: 0.0624
  time to fit residues: 13.9356
Evaluate side-chains
  136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  478 SER
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  560 ILE
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  644 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:   10.0000
   chunk 108 optimal weight:    0.8980
   chunk 112 optimal weight:   20.0000
   chunk 18 optimal weight:    4.9990
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 588 GLN
B 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.102794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.079385 restraints weight = 39651.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.081638 restraints weight = 22943.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.083078 restraints weight = 15642.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.084029 restraints weight = 12042.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.084609 restraints weight = 10172.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9106  Z= 0.140
  Angle     :  0.720  12.956  12342  Z= 0.343
  Chirality :  0.043   0.222   1514
  Planarity :  0.003   0.032   1544
  Dihedral  :  4.974  49.639   1238
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.97 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.58 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.25), residues: 1122
  helix:  1.19 (0.21), residues: 640
  sheet: -1.29 (0.80), residues: 34
  loop : -1.56 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 627 
 TYR   0.026   0.001   TYR B 559 
 PHE   0.009   0.001   PHE B 256 
 TRP   0.004   0.001   TRP B 408 
 HIS   0.002   0.001   HIS A 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9106)
  covalent geometry    : angle       0.71985 (12342)
  hydrogen bonds       : bond        0.06100 (  457)
  hydrogen bonds       : angle       4.27414 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 113
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4645 (t80) cc_final: 0.3998 (m-80)
REVERT: A  409 MET cc_start: 0.8007 (tpp) cc_final: 0.7764 (tpt)
REVERT: A  561 ASN cc_start: 0.8928 (t0) cc_final: 0.8394 (t0)
REVERT: A  662 ASP cc_start: 0.9169 (m-30) cc_final: 0.8795 (p0)
REVERT: A  679 THR cc_start: 0.6410 (OUTLIER) cc_final: 0.6090 (t)
REVERT: B  300 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9111 (mm)
REVERT: B  559 TYR cc_start: 0.8503 (p90) cc_final: 0.7705 (p90)
REVERT: B  561 ASN cc_start: 0.9076 (t0) cc_final: 0.8418 (t0)
REVERT: B  679 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.6094 (t)
  outliers start: 38
  outliers final: 29
  residues processed: 143
  average time/residue: 0.0552
  time to fit residues: 12.4495
Evaluate side-chains
  136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  560 ILE
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  662 ASP
Chi-restraints excluded: chain B residue  679 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 85 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 44 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 182 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.100269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.077017 restraints weight = 40574.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.079211 restraints weight = 23448.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.080577 restraints weight = 16031.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.081490 restraints weight = 12452.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.082047 restraints weight = 10589.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9106  Z= 0.182
  Angle     :  0.772  12.792  12342  Z= 0.375
  Chirality :  0.045   0.312   1514
  Planarity :  0.003   0.034   1544
  Dihedral  :  5.230  52.973   1238
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.24 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.68 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.25), residues: 1122
  helix:  1.04 (0.21), residues: 628
  sheet: -1.83 (0.78), residues: 36
  loop : -1.39 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 606 
 TYR   0.029   0.002   TYR A 568 
 PHE   0.009   0.001   PHE B 382 
 TRP   0.005   0.002   TRP A 408 
 HIS   0.003   0.001   HIS B 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9106)
  covalent geometry    : angle       0.77196 (12342)
  hydrogen bonds       : bond        0.06863 (  457)
  hydrogen bonds       : angle       4.49113 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 105
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4712 (t80) cc_final: 0.4098 (m-80)
REVERT: A  561 ASN cc_start: 0.8984 (t0) cc_final: 0.8408 (t0)
REVERT: A  607 MET cc_start: 0.8586 (ppp) cc_final: 0.8295 (pmm)
REVERT: A  662 ASP cc_start: 0.9180 (m-30) cc_final: 0.8778 (p0)
REVERT: A  679 THR cc_start: 0.6456 (OUTLIER) cc_final: 0.6104 (t)
REVERT: B  561 ASN cc_start: 0.9145 (t0) cc_final: 0.8712 (t0)
REVERT: B  679 THR cc_start: 0.6459 (OUTLIER) cc_final: 0.6142 (t)
  outliers start: 39
  outliers final: 28
  residues processed: 137
  average time/residue: 0.0545
  time to fit residues: 11.7918
Evaluate side-chains
  133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  560 ILE
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  662 ASP
Chi-restraints excluded: chain B residue  679 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0570
   chunk 6 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.9702

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

Flipped N/Q/H residues before XYZ refinement:
B 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.104403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.081140 restraints weight = 39320.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.083461 restraints weight = 22664.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.084956 restraints weight = 15416.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.085933 restraints weight = 11837.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.086524 restraints weight = 9970.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9106  Z= 0.129
  Angle     :  0.752  12.789  12342  Z= 0.347
  Chirality :  0.043   0.256   1514
  Planarity :  0.003   0.032   1544
  Dihedral  :  4.906  51.630   1238
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.15 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 25.00 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.25), residues: 1122
  helix:  1.29 (0.22), residues: 632
  sheet: -1.38 (0.80), residues: 34
  loop : -1.45 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 627 
 TYR   0.028   0.001   TYR B 559 
 PHE   0.012   0.001   PHE B 256 
 TRP   0.008   0.002   TRP B 408 
 HIS   0.002   0.000   HIS B 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9106)
  covalent geometry    : angle       0.75200 (12342)
  hydrogen bonds       : bond        0.05797 (  457)
  hydrogen bonds       : angle       4.14106 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4416 (t80) cc_final: 0.3814 (m-80)
REVERT: A  561 ASN cc_start: 0.8765 (t0) cc_final: 0.8272 (t0)
REVERT: A  662 ASP cc_start: 0.9140 (m-30) cc_final: 0.8758 (p0)
REVERT: A  679 THR cc_start: 0.6329 (OUTLIER) cc_final: 0.5987 (t)
REVERT: B  561 ASN cc_start: 0.9021 (t0) cc_final: 0.8354 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0614
  time to fit residues: 12.9532
Evaluate side-chains
  123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  560 ILE
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  644 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 95 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.6386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.103372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.080277 restraints weight = 39218.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.082543 restraints weight = 22645.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.083954 restraints weight = 15435.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.084904 restraints weight = 11960.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.085470 restraints weight = 10112.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9106  Z= 0.132
  Angle     :  0.777  13.884  12342  Z= 0.358
  Chirality :  0.045   0.350   1514
  Planarity :  0.003   0.033   1544
  Dihedral  :  4.855  48.530   1238
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.97 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 26.01 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.25), residues: 1122
  helix:  1.36 (0.22), residues: 622
  sheet: -1.40 (0.80), residues: 34
  loop : -1.28 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 627 
 TYR   0.030   0.001   TYR B 559 
 PHE   0.015   0.001   PHE B 256 
 TRP   0.006   0.001   TRP B 408 
 HIS   0.002   0.000   HIS B 490 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9106)
  covalent geometry    : angle       0.77669 (12342)
  hydrogen bonds       : bond        0.05766 (  457)
  hydrogen bonds       : angle       4.12216 ( 1338)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4442 (t80) cc_final: 0.3916 (m-80)
REVERT: A  561 ASN cc_start: 0.8809 (t0) cc_final: 0.8338 (t0)
REVERT: A  679 THR cc_start: 0.6301 (OUTLIER) cc_final: 0.5957 (t)
REVERT: B  561 ASN cc_start: 0.9001 (t0) cc_final: 0.8332 (t0)
  outliers start: 22
  outliers final: 21
  residues processed: 126
  average time/residue: 0.0706
  time to fit residues: 13.8570
Evaluate side-chains
  126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  290 VAL
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  560 ILE
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  344 SER
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  644 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:    0.0010
   chunk 42 optimal weight:    0.9990
   chunk 61 optimal weight:   20.0000
   chunk 82 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:   20.0000
   overall best weight:    0.6988

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.106363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.084068 restraints weight = 39189.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.086434 restraints weight = 22081.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.087932 restraints weight = 14752.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.088892 restraints weight = 11227.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.089439 restraints weight = 9436.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9106  Z= 0.125
  Angle     :  0.764  14.461  12342  Z= 0.349
  Chirality :  0.044   0.292   1514
  Planarity :  0.003   0.033   1544
  Dihedral  :  4.670  48.454   1238
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.33 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 26.01 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.25), residues: 1122
  helix:  1.45 (0.22), residues: 622
  sheet: -1.27 (0.80), residues: 34
  loop : -1.43 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 627 
 TYR   0.026   0.001   TYR B 559 
 PHE   0.014   0.001   PHE B 256 
 TRP   0.010   0.002   TRP B 408 
 HIS   0.002   0.000   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9106)
  covalent geometry    : angle       0.76426 (12342)
  hydrogen bonds       : bond        0.05052 (  457)
  hydrogen bonds       : angle       4.01973 ( 1338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1478.41 seconds
wall clock time: 26 minutes 18.15 seconds (1578.15 seconds total)