Starting phenix.real_space_refine
on Thu Feb 13 13:19:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hf7_34715/02_2025/8hf7_34715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hf7_34715/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hf7_34715/02_2025/8hf7_34715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hf7_34715/02_2025/8hf7_34715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hf7_34715/02_2025/8hf7_34715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hf7_34715/02_2025/8hf7_34715.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.67, per 1000 atoms: 0.63
  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: 2.15
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.94
  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: 2.58

  Time building geometry restraints manager: 2.53 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: 0.04
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:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.870
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.790
-------------------------------------------------------------------------------
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= 0.402
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.003   0.001   TRP A 408 
 HIS   0.002   0.001   HIS A 676 
 PHE   0.041   0.002   PHE A 257 
 TYR   0.023   0.002   TYR A 559 
 ARG   0.004   0.001   ARG A 629 

*********************** 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  : 1.062 
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: 0.1782
  time to fit residues: 46.7940
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  : 1.006 
-------------------------------------------------------------------------------
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 96 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 89 optimal weight:    8.9990
   chunk 34 optimal weight:   30.0000
   chunk 54 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4004 r_free = 0.4004 target = 0.102478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.078820 restraints weight = 39620.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.081037 restraints weight = 22820.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.082446 restraints weight = 15644.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9106  Z= 0.316
  Angle     :  0.806   9.787  12342  Z= 0.413
  Chirality :  0.045   0.240   1514
  Planarity :  0.004   0.032   1544
  Dihedral  :  6.143  50.682   1242
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.08 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.25 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.24), residues: 1122
  helix:  0.11 (0.21), residues: 632
  sheet: -1.08 (0.76), residues: 34
  loop : -1.78 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B 408 
 HIS   0.002   0.001   HIS A 676 
 PHE   0.016   0.002   PHE B 257 
 TYR   0.026   0.002   TYR B 188 
 ARG   0.007   0.001   ARG B 593 

*********************** 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
  157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9029 (mm)
REVERT: A  529 MET cc_start: 0.9559 (pmm) cc_final: 0.9199 (pmm)
REVERT: A  561 ASN cc_start: 0.8835 (t0) cc_final: 0.8220 (t0)
REVERT: B  300 LEU cc_start: 0.9219 (mm) cc_final: 0.9001 (mm)
REVERT: B  529 MET cc_start: 0.9513 (pmm) cc_final: 0.9129 (pmm)
  outliers start: 26
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1620
  time to fit residues: 37.0073
Evaluate side-chains
  129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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  404 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  490 HIS
Chi-restraints excluded: chain A residue  560 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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0040
   chunk 81 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 97 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    1.9398

-------------------------------------------------------------------------------
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 = 0.4033 r_free = 0.4033 target = 0.104220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.081356 restraints weight = 38876.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.083667 restraints weight = 22137.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.085146 restraints weight = 14907.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9106  Z= 0.189
  Angle     :  0.673   9.606  12342  Z= 0.334
  Chirality :  0.042   0.226   1514
  Planarity :  0.003   0.030   1544
  Dihedral  :  5.111  35.867   1238
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.44 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.80 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.25), residues: 1122
  helix:  0.71 (0.21), residues: 640
  sheet: -1.26 (0.75), residues: 34
  loop : -1.76 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 408 
 HIS   0.002   0.001   HIS A 676 
 PHE   0.013   0.001   PHE A 257 
 TYR   0.030   0.002   TYR B 559 
 ARG   0.004   0.000   ARG B 593 

*********************** 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
  154 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8996 (mm)
REVERT: A  409 MET cc_start: 0.7814 (tpp) cc_final: 0.7543 (tpt)
REVERT: A  561 ASN cc_start: 0.8851 (t0) cc_final: 0.8255 (t0)
REVERT: B  300 LEU cc_start: 0.9220 (mm) cc_final: 0.9008 (mm)
REVERT: B  415 MET cc_start: 0.8984 (tpt) cc_final: 0.8776 (tpt)
REVERT: B  529 MET cc_start: 0.9416 (pmm) cc_final: 0.9098 (pmm)
  outliers start: 26
  outliers final: 20
  residues processed: 146
  average time/residue: 0.1581
  time to fit residues: 34.9655
Evaluate side-chains
  132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
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  490 HIS
Chi-restraints excluded: chain A residue  525 THR
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  192 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  644 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 92 optimal weight:   30.0000
   chunk 48 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 49 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   overall best weight:    1.8984

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.104374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.081570 restraints weight = 39034.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.083865 restraints weight = 22051.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.085343 restraints weight = 14858.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9106  Z= 0.179
  Angle     :  0.681  13.020  12342  Z= 0.329
  Chirality :  0.042   0.196   1514
  Planarity :  0.003   0.030   1544
  Dihedral  :  4.892  34.891   1238
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.70 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.32 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.25), residues: 1122
  helix:  0.91 (0.21), residues: 642
  sheet: -1.22 (0.76), residues: 34
  loop : -1.63 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A 408 
 HIS   0.002   0.000   HIS A 676 
 PHE   0.011   0.001   PHE B 257 
 TYR   0.028   0.002   TYR B 559 
 ARG   0.003   0.000   ARG B 593 

*********************** 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
  161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 THR cc_start: 0.8862 (m) cc_final: 0.8529 (p)
REVERT: A  187 TYR cc_start: 0.4573 (t80) cc_final: 0.3846 (m-80)
REVERT: A  300 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9016 (mm)
REVERT: A  409 MET cc_start: 0.7982 (tpp) cc_final: 0.7637 (tpt)
REVERT: A  561 ASN cc_start: 0.8917 (t0) cc_final: 0.8310 (t0)
REVERT: A  662 ASP cc_start: 0.9165 (m-30) cc_final: 0.8771 (p0)
REVERT: B  300 LEU cc_start: 0.9295 (mm) cc_final: 0.9045 (mm)
REVERT: B  529 MET cc_start: 0.9425 (pmm) cc_final: 0.9142 (pmm)
  outliers start: 40
  outliers final: 31
  residues processed: 151
  average time/residue: 0.1529
  time to fit residues: 35.2353
Evaluate side-chains
  146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
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  232 VAL
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  282 THR
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  560 ILE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  644 ILE
Chi-restraints excluded: chain B residue  178 VAL
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  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  490 HIS
Chi-restraints excluded: chain B residue  525 THR
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  609 LEU
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 60 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:   20.0000
   chunk 53 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    7.9990
   chunk 44 optimal weight:   20.0000
   chunk 99 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.105897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.082484 restraints weight = 39074.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.084867 restraints weight = 22214.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.086373 restraints weight = 14909.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9106  Z= 0.158
  Angle     :  0.682  12.636  12342  Z= 0.322
  Chirality :  0.042   0.194   1514
  Planarity :  0.003   0.032   1544
  Dihedral  :  4.715  34.230   1238
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.79 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.96 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.25), residues: 1122
  helix:  1.13 (0.22), residues: 640
  sheet: -1.14 (0.78), residues: 34
  loop : -1.63 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 408 
 HIS   0.002   0.000   HIS A 676 
 PHE   0.011   0.001   PHE B 257 
 TYR   0.028   0.001   TYR B 559 
 ARG   0.003   0.000   ARG B 593 

*********************** 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
  152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 1.178 
Fit side-chains
REVERT: A  187 TYR cc_start: 0.4475 (t80) cc_final: 0.3699 (m-80)
REVERT: A  300 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9087 (mm)
REVERT: A  409 MET cc_start: 0.7898 (tpp) cc_final: 0.7661 (tpt)
REVERT: A  561 ASN cc_start: 0.8820 (t0) cc_final: 0.8242 (t0)
REVERT: A  607 MET cc_start: 0.8725 (ppp) cc_final: 0.8502 (ppp)
REVERT: A  662 ASP cc_start: 0.9158 (m-30) cc_final: 0.8785 (p0)
REVERT: B  300 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9102 (mm)
  outliers start: 28
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1649
  time to fit residues: 36.5319
Evaluate side-chains
  122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  282 THR
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  525 THR
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  351 ILE
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  644 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 55 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    2.0788

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.104096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.081665 restraints weight = 38998.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.083912 restraints weight = 22108.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.085326 restraints weight = 14942.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9106  Z= 0.186
  Angle     :  0.708  12.837  12342  Z= 0.339
  Chirality :  0.042   0.212   1514
  Planarity :  0.003   0.034   1544
  Dihedral  :  4.631  33.086   1236
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.06 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1122
  helix:  1.19 (0.22), residues: 632
  sheet: -1.20 (0.79), residues: 34
  loop : -1.45 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 408 
 HIS   0.002   0.000   HIS A 676 
 PHE   0.009   0.001   PHE B 257 
 TYR   0.033   0.001   TYR B 188 
 ARG   0.002   0.000   ARG B 593 

*********************** 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
  153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4472 (t80) cc_final: 0.3811 (m-80)
REVERT: A  409 MET cc_start: 0.7940 (tpp) cc_final: 0.7680 (tpt)
REVERT: A  463 LEU cc_start: 0.8895 (tt) cc_final: 0.8672 (pp)
REVERT: A  561 ASN cc_start: 0.8894 (t0) cc_final: 0.8337 (t0)
REVERT: A  662 ASP cc_start: 0.9157 (m-30) cc_final: 0.8783 (p0)
REVERT: A  679 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6105 (t)
REVERT: B  300 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9098 (mm)
REVERT: B  561 ASN cc_start: 0.9062 (t0) cc_final: 0.8391 (t0)
  outliers start: 38
  outliers final: 28
  residues processed: 143
  average time/residue: 0.1524
  time to fit residues: 33.4222
Evaluate side-chains
  139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
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  282 THR
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  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  171 ILE
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  271 ASP
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  644 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 110 optimal weight:   30.0000
   chunk 83 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.103979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.080527 restraints weight = 39451.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.082857 restraints weight = 22522.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.084362 restraints weight = 15184.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9106  Z= 0.180
  Angle     :  0.704  13.243  12342  Z= 0.336
  Chirality :  0.042   0.213   1514
  Planarity :  0.003   0.034   1544
  Dihedral  :  4.632  33.858   1236
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.79 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.48 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.25), residues: 1122
  helix:  1.20 (0.21), residues: 640
  sheet: -1.25 (0.79), residues: 34
  loop : -1.56 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 408 
 HIS   0.001   0.000   HIS B 490 
 PHE   0.008   0.001   PHE B 257 
 TYR   0.035   0.001   TYR B 188 
 ARG   0.002   0.000   ARG B 627 

*********************** 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
  153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  179 THR cc_start: 0.8806 (m) cc_final: 0.8453 (p)
REVERT: A  187 TYR cc_start: 0.4544 (t80) cc_final: 0.3865 (m-80)
REVERT: A  409 MET cc_start: 0.7962 (tpp) cc_final: 0.7702 (tpt)
REVERT: A  463 LEU cc_start: 0.8945 (tt) cc_final: 0.8721 (pp)
REVERT: A  561 ASN cc_start: 0.8855 (t0) cc_final: 0.8304 (t0)
REVERT: A  662 ASP cc_start: 0.9157 (m-30) cc_final: 0.8794 (p0)
REVERT: A  679 THR cc_start: 0.6420 (OUTLIER) cc_final: 0.6116 (t)
REVERT: B  300 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9121 (mm)
REVERT: B  561 ASN cc_start: 0.9075 (t0) cc_final: 0.8400 (t0)
  outliers start: 38
  outliers final: 28
  residues processed: 145
  average time/residue: 0.1536
  time to fit residues: 34.1621
Evaluate side-chains
  137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
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  282 THR
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  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  644 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 106 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0970
   chunk 90 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 44 optimal weight:   20.0000
   overall best weight:    3.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 588 GLN
B 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.100701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.077359 restraints weight = 40496.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.079593 restraints weight = 23307.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.081034 restraints weight = 15821.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9106  Z= 0.243
  Angle     :  0.776  13.478  12342  Z= 0.377
  Chirality :  0.044   0.252   1514
  Planarity :  0.003   0.037   1544
  Dihedral  :  4.942  35.172   1236
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.15 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.25), residues: 1122
  helix:  0.96 (0.21), residues: 628
  sheet: -1.81 (0.79), residues: 36
  loop : -1.36 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 408 
 HIS   0.003   0.001   HIS B 490 
 PHE   0.010   0.001   PHE B 382 
 TYR   0.032   0.002   TYR A 568 
 ARG   0.002   0.001   ARG A 606 

*********************** 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
  148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4761 (t80) cc_final: 0.4131 (m-80)
REVERT: A  561 ASN cc_start: 0.9014 (t0) cc_final: 0.8488 (t0)
REVERT: A  662 ASP cc_start: 0.9194 (m-30) cc_final: 0.8800 (p0)
REVERT: A  679 THR cc_start: 0.6400 (OUTLIER) cc_final: 0.6048 (t)
REVERT: B  561 ASN cc_start: 0.9167 (t0) cc_final: 0.8739 (t0)
REVERT: B  662 ASP cc_start: 0.9505 (OUTLIER) cc_final: 0.8995 (p0)
REVERT: B  679 THR cc_start: 0.6346 (OUTLIER) cc_final: 0.6021 (t)
  outliers start: 39
  outliers final: 29
  residues processed: 140
  average time/residue: 0.1611
  time to fit residues: 34.5641
Evaluate side-chains
  138 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
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  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  551 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  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 103 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0980
   chunk 72 optimal weight:    0.5980
   chunk 93 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 96 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    2.1386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.102440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.079188 restraints weight = 40116.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.081416 restraints weight = 23199.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.082826 restraints weight = 15837.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9106  Z= 0.201
  Angle     :  0.763  13.106  12342  Z= 0.358
  Chirality :  0.044   0.279   1514
  Planarity :  0.003   0.032   1544
  Dihedral  :  4.772  34.385   1236
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.15 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 24.80 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1122
  helix:  1.06 (0.21), residues: 642
  sheet: -1.46 (0.80), residues: 34
  loop : -1.44 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 408 
 HIS   0.002   0.001   HIS B 490 
 PHE   0.010   0.001   PHE A 256 
 TYR   0.028   0.001   TYR B 559 
 ARG   0.002   0.000   ARG B 627 

*********************** 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: 30
    poor density    : 106
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4695 (t80) cc_final: 0.4038 (m-80)
REVERT: A  463 LEU cc_start: 0.9040 (tt) cc_final: 0.8811 (pp)
REVERT: A  561 ASN cc_start: 0.8953 (t0) cc_final: 0.8462 (t0)
REVERT: A  662 ASP cc_start: 0.9195 (m-30) cc_final: 0.8828 (p0)
REVERT: A  679 THR cc_start: 0.6377 (OUTLIER) cc_final: 0.6027 (t)
REVERT: B  561 ASN cc_start: 0.9108 (t0) cc_final: 0.8466 (t0)
REVERT: B  679 THR cc_start: 0.6365 (OUTLIER) cc_final: 0.6055 (t)
  outliers start: 30
  outliers final: 25
  residues processed: 133
  average time/residue: 0.1622
  time to fit residues: 33.2925
Evaluate side-chains
  131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
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  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  525 THR
Chi-restraints excluded: chain A residue  551 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  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  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  679 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 12 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   chunk 101 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 56 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   overall best weight:    2.7188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.101356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.078181 restraints weight = 39875.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.080386 restraints weight = 23077.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.081767 restraints weight = 15761.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.4097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9106  Z= 0.220
  Angle     :  0.788  13.484  12342  Z= 0.371
  Chirality :  0.045   0.344   1514
  Planarity :  0.003   0.036   1544
  Dihedral  :  4.836  33.442   1236
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.51 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 24.90 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.25), residues: 1122
  helix:  1.08 (0.21), residues: 632
  sheet: -1.89 (0.78), residues: 36
  loop : -1.30 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 408 
 HIS   0.003   0.001   HIS B 490 
 PHE   0.009   0.001   PHE A 256 
 TYR   0.029   0.001   TYR B 559 
 ARG   0.002   0.000   ARG A 627 

********************** 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
  134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TYR cc_start: 0.4679 (t80) cc_final: 0.4098 (m-80)
REVERT: A  561 ASN cc_start: 0.8944 (t0) cc_final: 0.8423 (t0)
REVERT: A  679 THR cc_start: 0.6394 (OUTLIER) cc_final: 0.6036 (t)
REVERT: B  561 ASN cc_start: 0.9132 (t0) cc_final: 0.8689 (t0)
REVERT: B  679 THR cc_start: 0.6365 (OUTLIER) cc_final: 0.6032 (t)
  outliers start: 32
  outliers final: 29
  residues processed: 129
  average time/residue: 0.1675
  time to fit residues: 33.0183
Evaluate side-chains
  132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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  551 ILE
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  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  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  679 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0470
   chunk 67 optimal weight:    0.7980
   chunk 11 optimal weight:    0.2980
   chunk 76 optimal weight:    8.9990
   chunk 69 optimal weight:    9.9990
   overall best weight:    0.5678

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.105832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.083385 restraints weight = 38830.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.085734 restraints weight = 21941.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.087238 restraints weight = 14669.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9106  Z= 0.173
  Angle     :  0.769  13.481  12342  Z= 0.351
  Chirality :  0.044   0.286   1514
  Planarity :  0.003   0.031   1544
  Dihedral  :  4.514  31.535   1236
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.97 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 26.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1122
  helix:  1.22 (0.22), residues: 644
  sheet: -1.44 (0.78), residues: 34
  loop : -1.52 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 408 
 HIS   0.001   0.001   HIS A 676 
 PHE   0.012   0.001   PHE A 256 
 TYR   0.026   0.001   TYR B 559 
 ARG   0.002   0.000   ARG A 627 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2774.57 seconds
wall clock time: 50 minutes 44.26 seconds (3044.26 seconds total)