Starting phenix.real_space_refine
on Tue Jul 29 16:08:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xy1_33507/07_2025/7xy1_33507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xy1_33507/07_2025/7xy1_33507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xy1_33507/07_2025/7xy1_33507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xy1_33507/07_2025/7xy1_33507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xy1_33507/07_2025/7xy1_33507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xy1_33507/07_2025/7xy1_33507.cif"
  }
  resolution = 3.3
  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=   0.005
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      48      5.16       5
     C    7143      2.51       5
     N    2076      2.21       5
     O    2283      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11550
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 3850
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 16, 'TRANS': 495}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 7.49, per 1000 atoms: 0.65
  Number of scatterers: 11550
  At special positions: 0
  Unit cell: (83.7876, 80.565, 150.388, 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      48     16.00
     O    2283      8.00
     N    2076      7.00
     C    7143      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: 2.90
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2730

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 27 sheets defined
      9.0% alpha, 27.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 283 through 292
      removed outlier: 3.515A  pdb=" N   LEU A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 301
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 319 through 329
      removed outlier: 4.064A  pdb=" N   GLY A 329 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 4.217A  pdb=" N   PHE A 370 " --> pdb=" O   ASP A 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 276
    Processing helix  chain 'B' and resid 283 through 292
      removed outlier: 3.515A  pdb=" N   LEU B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 301
    Processing helix  chain 'B' and resid 302 through 312
    Processing helix  chain 'B' and resid 319 through 329
      removed outlier: 4.064A  pdb=" N   GLY B 329 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 370
      removed outlier: 4.217A  pdb=" N   PHE B 370 " --> pdb=" O   ASP B 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 276
    Processing helix  chain 'C' and resid 283 through 292
      removed outlier: 3.515A  pdb=" N   LEU C 291 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG C 292 " --> pdb=" O   LEU C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 301
    Processing helix  chain 'C' and resid 302 through 312
    Processing helix  chain 'C' and resid 319 through 329
      removed outlier: 4.064A  pdb=" N   GLY C 329 " --> pdb=" O   ALA C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 366 through 370
      removed outlier: 4.217A  pdb=" N   PHE C 370 " --> pdb=" O   ASP C 367 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 295 through 296
      removed outlier: 6.594A  pdb=" N   VAL A 295 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ILE A 333 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LEU A 353 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA A 395 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   CYS A 425 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL A 398 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   TYR A 428 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   PHE A 400 " --> pdb=" O   TYR A 428 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ILE A 377 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296
      removed outlier: 6.594A  pdb=" N   VAL A 295 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ILE A 333 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LEU A 353 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA A 395 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   CYS A 425 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   GLY A 421 " --> pdb=" O   PHE A 445 " (cutoff:3.500A)
      removed outlier: 9.175A  pdb=" N   PHE A 447 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   PHE A 423 " --> pdb=" O   PHE A 447 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   ASN A 449 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   CYS A 425 " --> pdb=" O   ASN A 449 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ASN A 451 " --> pdb=" O   CYS A 425 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   PHE A 427 " --> pdb=" O   ASN A 451 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346
      removed outlier: 6.732A  pdb=" N   VAL A 345 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLN A 411 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 458
      removed outlier: 5.575A  pdb=" N   ILE A 457 " --> pdb=" O   MET A 479 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ILE A 555 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ALA A 592 " --> pdb=" O   ILE A 555 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   PHE A 557 " --> pdb=" O   ALA A 592 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 465
      removed outlier: 6.176A  pdb=" N   LEU A 562 " --> pdb=" O   GLU A 600 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   SER A 602 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   MET A 564 " --> pdb=" O   SER A 602 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA7, first strand: chain 'A' and resid 640 through 643
    Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655
      removed outlier: 3.559A  pdb=" N   ASP A 682 " --> pdb=" O   LYS A 776 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   GLY A 697 " --> pdb=" O   SER A 720 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   SER A 720 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ILE A 699 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   VAL A 718 " --> pdb=" O   ILE A 699 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   THR A 701 " --> pdb=" O   VAL A 716 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 664 through 669
    Processing sheet with id=AB1, first strand: chain 'B' and resid 295 through 296
      removed outlier: 6.595A  pdb=" N   VAL B 295 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ILE B 333 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU B 353 " --> pdb=" O   GLU B 396 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   CYS B 425 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL B 398 " --> pdb=" O   GLY B 426 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   TYR B 428 " --> pdb=" O   VAL B 398 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   PHE B 400 " --> pdb=" O   TYR B 428 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ILE B 377 " --> pdb=" O   ASP B 401 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 295 through 296
      removed outlier: 6.595A  pdb=" N   VAL B 295 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ILE B 333 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU B 353 " --> pdb=" O   GLU B 396 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   CYS B 425 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   GLY B 421 " --> pdb=" O   PHE B 445 " (cutoff:3.500A)
      removed outlier: 9.175A  pdb=" N   PHE B 447 " --> pdb=" O   GLY B 421 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   PHE B 423 " --> pdb=" O   PHE B 447 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   ASN B 449 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   CYS B 425 " --> pdb=" O   ASN B 449 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ASN B 451 " --> pdb=" O   CYS B 425 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   PHE B 427 " --> pdb=" O   ASN B 451 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 345 through 346
      removed outlier: 6.732A  pdb=" N   VAL B 345 " --> pdb=" O   LEU B 388 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLN B 411 " --> pdb=" O   PHE B 387 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 457 through 458
      removed outlier: 5.575A  pdb=" N   ILE B 457 " --> pdb=" O   MET B 479 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B 555 " --> pdb=" O   ARG B 590 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ALA B 592 " --> pdb=" O   ILE B 555 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   PHE B 557 " --> pdb=" O   ALA B 592 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 464 through 465
      removed outlier: 6.176A  pdb=" N   LEU B 562 " --> pdb=" O   GLU B 600 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   SER B 602 " --> pdb=" O   LEU B 562 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   MET B 564 " --> pdb=" O   SER B 602 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 538 through 539
    Processing sheet with id=AB7, first strand: chain 'B' and resid 640 through 643
    Processing sheet with id=AB8, first strand: chain 'B' and resid 654 through 655
      removed outlier: 3.559A  pdb=" N   ASP B 682 " --> pdb=" O   LYS B 776 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   GLY B 697 " --> pdb=" O   SER B 720 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   SER B 720 " --> pdb=" O   GLY B 697 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ILE B 699 " --> pdb=" O   VAL B 718 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   VAL B 718 " --> pdb=" O   ILE B 699 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   THR B 701 " --> pdb=" O   VAL B 716 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 664 through 669
    Processing sheet with id=AC1, first strand: chain 'C' and resid 295 through 296
      removed outlier: 6.594A  pdb=" N   VAL C 295 " --> pdb=" O   ILE C 334 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ILE C 333 " --> pdb=" O   PHE C 354 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU C 353 " --> pdb=" O   GLU C 396 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA C 395 " --> pdb=" O   PHE C 423 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   CYS C 425 " --> pdb=" O   ALA C 395 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL C 398 " --> pdb=" O   GLY C 426 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   TYR C 428 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   PHE C 400 " --> pdb=" O   TYR C 428 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ILE C 377 " --> pdb=" O   ASP C 401 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 295 through 296
      removed outlier: 6.594A  pdb=" N   VAL C 295 " --> pdb=" O   ILE C 334 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ILE C 333 " --> pdb=" O   PHE C 354 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU C 353 " --> pdb=" O   GLU C 396 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   ALA C 395 " --> pdb=" O   PHE C 423 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   CYS C 425 " --> pdb=" O   ALA C 395 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   GLY C 421 " --> pdb=" O   PHE C 445 " (cutoff:3.500A)
      removed outlier: 9.175A  pdb=" N   PHE C 447 " --> pdb=" O   GLY C 421 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   PHE C 423 " --> pdb=" O   PHE C 447 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   ASN C 449 " --> pdb=" O   PHE C 423 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   CYS C 425 " --> pdb=" O   ASN C 449 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ASN C 451 " --> pdb=" O   CYS C 425 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   PHE C 427 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 345 through 346
      removed outlier: 6.733A  pdb=" N   VAL C 345 " --> pdb=" O   LEU C 388 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLN C 411 " --> pdb=" O   PHE C 387 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 457 through 458
      removed outlier: 5.575A  pdb=" N   ILE C 457 " --> pdb=" O   MET C 479 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ILE C 555 " --> pdb=" O   ARG C 590 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ALA C 592 " --> pdb=" O   ILE C 555 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   PHE C 557 " --> pdb=" O   ALA C 592 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 464 through 465
      removed outlier: 6.177A  pdb=" N   LEU C 562 " --> pdb=" O   GLU C 600 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   SER C 602 " --> pdb=" O   LEU C 562 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   MET C 564 " --> pdb=" O   SER C 602 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 538 through 539
    Processing sheet with id=AC7, first strand: chain 'C' and resid 640 through 643
    Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655
      removed outlier: 3.559A  pdb=" N   ASP C 682 " --> pdb=" O   LYS C 776 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   GLY C 697 " --> pdb=" O   SER C 720 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   SER C 720 " --> pdb=" O   GLY C 697 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ILE C 699 " --> pdb=" O   VAL C 718 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   VAL C 718 " --> pdb=" O   ILE C 699 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   THR C 701 " --> pdb=" O   VAL C 716 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 664 through 669

    264 hydrogen bonds defined for protein.
    702 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: 4.28

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1992
        1.32 -     1.44: 3269
        1.44 -     1.56: 6427
        1.56 -     1.68: 3
        1.68 -     1.81: 72
  Bond restraints: 11763
  Sorted by residual:
  bond pdb=" CA  CYS C 468 "
       pdb=" C   CYS C 468 "
    ideal  model  delta    sigma   weight residual
    1.527  1.477  0.050 1.35e-02 5.49e+03 1.36e+01
  bond pdb=" CA  CYS A 468 "
       pdb=" C   CYS A 468 "
    ideal  model  delta    sigma   weight residual
    1.527  1.477  0.050 1.35e-02 5.49e+03 1.36e+01
  bond pdb=" CA  CYS B 468 "
       pdb=" C   CYS B 468 "
    ideal  model  delta    sigma   weight residual
    1.527  1.477  0.050 1.35e-02 5.49e+03 1.36e+01
  bond pdb=" CA  SER A 530 "
       pdb=" C   SER A 530 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.043 1.19e-02 7.06e+03 1.29e+01
  bond pdb=" CA  SER C 530 "
       pdb=" C   SER C 530 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.043 1.19e-02 7.06e+03 1.29e+01
  ... (remaining 11758 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 15591
        2.24 -     4.48: 297
        4.48 -     6.72: 51
        6.72 -     8.96: 9
        8.96 -    11.20: 3
  Bond angle restraints: 15951
  Sorted by residual:
  angle pdb=" N   HIS B 476 "
        pdb=" CA  HIS B 476 "
        pdb=" C   HIS B 476 "
      ideal   model   delta    sigma   weight residual
     111.28  122.48  -11.20 1.09e+00 8.42e-01 1.06e+02
  angle pdb=" N   HIS C 476 "
        pdb=" CA  HIS C 476 "
        pdb=" C   HIS C 476 "
      ideal   model   delta    sigma   weight residual
     111.28  122.48  -11.20 1.09e+00 8.42e-01 1.06e+02
  angle pdb=" N   HIS A 476 "
        pdb=" CA  HIS A 476 "
        pdb=" C   HIS A 476 "
      ideal   model   delta    sigma   weight residual
     111.28  122.47  -11.19 1.09e+00 8.42e-01 1.05e+02
  angle pdb=" N   SER B 486 "
        pdb=" CA  SER B 486 "
        pdb=" CB  SER B 486 "
      ideal   model   delta    sigma   weight residual
     110.49  117.65   -7.16 1.69e+00 3.50e-01 1.80e+01
  angle pdb=" N   SER A 486 "
        pdb=" CA  SER A 486 "
        pdb=" CB  SER A 486 "
      ideal   model   delta    sigma   weight residual
     110.49  117.60   -7.11 1.69e+00 3.50e-01 1.77e+01
  ... (remaining 15946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.83: 6255
       16.83 -    33.66: 534
       33.66 -    50.49: 105
       50.49 -    67.31: 9
       67.31 -    84.14: 9
  Dihedral angle restraints: 6912
    sinusoidal: 2595
      harmonic: 4317
  Sorted by residual:
  dihedral pdb=" N   VAL A 661 "
           pdb=" C   VAL A 661 "
           pdb=" CA  VAL A 661 "
           pdb=" CB  VAL A 661 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.83  -12.43     0      2.50e+00 1.60e-01 2.47e+01
  dihedral pdb=" N   VAL B 661 "
           pdb=" C   VAL B 661 "
           pdb=" CA  VAL B 661 "
           pdb=" CB  VAL B 661 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.83  -12.43     0      2.50e+00 1.60e-01 2.47e+01
  dihedral pdb=" N   VAL C 661 "
           pdb=" C   VAL C 661 "
           pdb=" CA  VAL C 661 "
           pdb=" CB  VAL C 661 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.78  -12.38     0      2.50e+00 1.60e-01 2.45e+01
  ... (remaining 6909 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1568
       0.093 -    0.186: 169
       0.186 -    0.279: 18
       0.279 -    0.373: 4
       0.373 -    0.466: 8
  Chirality restraints: 1767
  Sorted by residual:
  chirality pdb=" CB  VAL B 661 "
            pdb=" CA  VAL B 661 "
            pdb=" CG1 VAL B 661 "
            pdb=" CG2 VAL B 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.16   -0.47 2.00e-01 2.50e+01 5.42e+00
  chirality pdb=" CB  VAL C 661 "
            pdb=" CA  VAL C 661 "
            pdb=" CG1 VAL C 661 "
            pdb=" CG2 VAL C 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.36e+00
  chirality pdb=" CB  VAL A 661 "
            pdb=" CA  VAL A 661 "
            pdb=" CG1 VAL A 661 "
            pdb=" CG2 VAL A 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.46 2.00e-01 2.50e+01 5.34e+00
  ... (remaining 1764 not shown)

  Planarity restraints: 2130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 483 "   -0.016 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   GLY B 483 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLY B 483 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA B 484 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 483 "   -0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   GLY A 483 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLY A 483 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA A 484 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 483 "   -0.016 2.00e-02 2.50e+03   3.31e-02 1.10e+01
        pdb=" C   GLY C 483 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLY C 483 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA C 484 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2127 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 192
        2.61 -     3.18: 10258
        3.18 -     3.75: 17520
        3.75 -     4.33: 25883
        4.33 -     4.90: 44207
  Nonbonded interactions: 98060
  Sorted by model distance:
  nonbonded pdb=" O   SER A 509 "
            pdb=" CG1 ILE A 510 "
     model   vdw
     2.035 3.440
  nonbonded pdb=" O   SER C 509 "
            pdb=" CG1 ILE C 510 "
     model   vdw
     2.035 3.440
  nonbonded pdb=" O   SER B 509 "
            pdb=" CG1 ILE B 510 "
     model   vdw
     2.036 3.440
  nonbonded pdb=" OG1 THR C 278 "
            pdb=" O   LEU C 282 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OG1 THR A 278 "
            pdb=" O   LEU A 282 "
     model   vdw
     2.222 3.040
  ... (remaining 98055 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  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:             0.020
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     30.840
  Find NCS groups from input model:        0.220
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
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      :  0.005   0.052  11763  Z= 0.304
  Angle     :  0.760  11.198  15951  Z= 0.453
  Chirality :  0.063   0.466   1767
  Planarity :  0.006   0.058   2130
  Dihedral  : 13.221  84.141   4182
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  8.43 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  0.32 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.44 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.21), residues: 1530
  helix: -0.25 (0.48), residues: 105
  sheet: -0.65 (0.25), residues: 546
  loop : -2.26 (0.18), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 496 
 HIS   0.009   0.003   HIS B 476 
 PHE   0.013   0.001   PHE A 521 
 TYR   0.012   0.001   TYR C 458 
 ARG   0.003   0.000   ARG B 619 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14895 (  264)
  hydrogen bonds       : angle       6.77278 (  702)
  covalent geometry    : bond        0.00462 (11763)
  covalent geometry    : angle       0.76011 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.393 
Fit side-chains
REVERT: A  670 CYS cc_start: 0.8277 (t) cc_final: 0.8021 (t)
REVERT: A  736 ASP cc_start: 0.7251 (t0) cc_final: 0.7034 (t0)
REVERT: B  600 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: B  670 CYS cc_start: 0.8251 (t) cc_final: 0.8039 (t)
  outliers start: 12
  outliers final: 6
  residues processed: 126
  average time/residue: 0.1751
  time to fit residues: 36.0429
Evaluate side-chains
  90 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 129 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   chunk 78 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 119 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 138 optimal weight:    2.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN
B 290 ASN
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
B 636 ASN
B 739 GLN
C 290 ASN
C 471 ASN
C 739 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.118500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.095318 restraints weight = 15065.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.46
r_work: 0.3147 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.076  11763  Z= 0.389
  Angle     :  0.797   7.736  15951  Z= 0.438
  Chirality :  0.056   0.311   1767
  Planarity :  0.007   0.076   2130
  Dihedral  :  6.264  42.755   1689
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.39 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.19 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.20), residues: 1530
  helix: -1.15 (0.45), residues: 105
  sheet: -1.01 (0.26), residues: 492
  loop : -2.44 (0.18), residues: 933

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 502 
 HIS   0.007   0.002   HIS B 476 
 PHE   0.023   0.003   PHE A 447 
 TYR   0.018   0.002   TYR C 505 
 ARG   0.005   0.001   ARG B 405 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03840 (  264)
  hydrogen bonds       : angle       5.74488 (  702)
  covalent geometry    : bond        0.00934 (11763)
  covalent geometry    : angle       0.79665 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 1.195 
Fit side-chains
REVERT: A  670 CYS cc_start: 0.8638 (t) cc_final: 0.8414 (t)
REVERT: A  770 ARG cc_start: 0.8012 (ttt-90) cc_final: 0.7796 (tmt170)
REVERT: C  498 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7437 (mp0)
  outliers start: 21
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1979
  time to fit residues: 29.2044
Evaluate side-chains
  82 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  498 GLU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  680 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 11 optimal weight:    0.0980
   chunk 36 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 145 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 149 optimal weight:    9.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.132283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.109943 restraints weight = 14417.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.42
r_work: 0.3284 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11763  Z= 0.102
  Angle     :  0.552   5.858  15951  Z= 0.302
  Chirality :  0.047   0.227   1767
  Planarity :  0.005   0.066   2130
  Dihedral  :  5.063  24.473   1689
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.76 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.76 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.21), residues: 1530
  helix: -1.06 (0.44), residues: 108
  sheet: -0.58 (0.25), residues: 507
  loop : -2.47 (0.18), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 502 
 HIS   0.003   0.001   HIS A 684 
 PHE   0.008   0.001   PHE C 521 
 TYR   0.020   0.001   TYR B 362 
 ARG   0.003   0.000   ARG B 770 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02859 (  264)
  hydrogen bonds       : angle       4.75359 (  702)
  covalent geometry    : bond        0.00216 (11763)
  covalent geometry    : angle       0.55205 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 1.298 
Fit side-chains
REVERT: C  600 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8197 (mt-10)
  outliers start: 22
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1997
  time to fit residues: 36.4521
Evaluate side-chains
  92 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  680 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 123 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 143 optimal weight:    9.9990
   chunk 110 optimal weight:    0.3980
   chunk 52 optimal weight:    0.1980
   chunk 102 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN
A 473 ASN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 GLN
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 ASN
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 471 ASN
C 473 ASN
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.123436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.100938 restraints weight = 14798.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.43
r_work: 0.3187 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  11763  Z= 0.261
  Angle     :  0.667   8.844  15951  Z= 0.364
  Chirality :  0.051   0.336   1767
  Planarity :  0.006   0.068   2130
  Dihedral  :  5.623  26.411   1689
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.52 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 11.65 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.20), residues: 1530
  helix: -1.16 (0.44), residues: 108
  sheet: -0.67 (0.26), residues: 444
  loop : -2.47 (0.18), residues: 978

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 502 
 HIS   0.004   0.002   HIS A 476 
 PHE   0.018   0.002   PHE A 447 
 TYR   0.018   0.002   TYR B 362 
 ARG   0.003   0.000   ARG B 519 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03214 (  264)
  hydrogen bonds       : angle       5.08538 (  702)
  covalent geometry    : bond        0.00626 (11763)
  covalent geometry    : angle       0.66727 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 81
  time to evaluate  : 1.326 
Fit side-chains
REVERT: A  424 LYS cc_start: 0.8344 (mttt) cc_final: 0.8117 (mttm)
REVERT: C  498 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7426 (mp0)
  outliers start: 36
  outliers final: 29
  residues processed: 107
  average time/residue: 0.1846
  time to fit residues: 31.9342
Evaluate side-chains
  102 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  681 PHE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  681 PHE
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  366 SER
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  498 GLU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  561 THR
Chi-restraints excluded: chain C residue  680 MET
Chi-restraints excluded: chain C residue  703 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 49 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 129 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 138 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 471 ASN
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.102539 restraints weight = 14693.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.47
r_work: 0.3288 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11763  Z= 0.119
  Angle     :  0.553   6.700  15951  Z= 0.301
  Chirality :  0.047   0.285   1767
  Planarity :  0.005   0.068   2130
  Dihedral  :  4.976  21.415   1689
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.76 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.62 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.20), residues: 1530
  helix: -1.10 (0.43), residues: 108
  sheet: -0.73 (0.24), residues: 510
  loop : -2.49 (0.18), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 502 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.008   0.001   PHE A 447 
 TYR   0.021   0.001   TYR B 362 
 ARG   0.002   0.000   ARG C 437 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02749 (  264)
  hydrogen bonds       : angle       4.58580 (  702)
  covalent geometry    : bond        0.00270 (11763)
  covalent geometry    : angle       0.55325 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 94
  time to evaluate  : 1.252 
Fit side-chains
REVERT: C  600 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8077 (mt-10)
  outliers start: 33
  outliers final: 27
  residues processed: 120
  average time/residue: 0.2125
  time to fit residues: 42.3161
Evaluate side-chains
  105 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 2.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  386 MET
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  386 MET
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  561 THR
Chi-restraints excluded: chain C residue  680 MET
Chi-restraints excluded: chain C residue  703 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 151 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 142 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 127 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0060
   chunk 146 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0870
   overall best weight:    1.7978

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN
A 473 ASN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 471 ASN
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.126543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.103969 restraints weight = 14625.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.43
r_work: 0.3246 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11763  Z= 0.163
  Angle     :  0.577   6.477  15951  Z= 0.315
  Chirality :  0.048   0.289   1767
  Planarity :  0.005   0.065   2130
  Dihedral  :  5.123  21.039   1686
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.00 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.35 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.20), residues: 1530
  helix: -0.99 (0.44), residues: 108
  sheet: -0.62 (0.24), residues: 498
  loop : -2.50 (0.18), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 476 
 PHE   0.014   0.001   PHE B 755 
 TYR   0.014   0.001   TYR B 362 
 ARG   0.002   0.000   ARG C 519 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02837 (  264)
  hydrogen bonds       : angle       4.65008 (  702)
  covalent geometry    : bond        0.00383 (11763)
  covalent geometry    : angle       0.57662 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 78
  time to evaluate  : 1.168 
Fit side-chains
REVERT: C  600 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8079 (mt-10)
  outliers start: 42
  outliers final: 29
  residues processed: 111
  average time/residue: 0.1496
  time to fit residues: 28.3834
Evaluate side-chains
  103 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  680 MET
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  366 SER
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  561 THR
Chi-restraints excluded: chain C residue  680 MET
Chi-restraints excluded: chain C residue  703 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 138 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 146 optimal weight:   10.0000
   chunk 131 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 141 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.099667 restraints weight = 15055.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.47
r_work: 0.3227 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11763  Z= 0.182
  Angle     :  0.602   7.815  15951  Z= 0.328
  Chirality :  0.049   0.302   1767
  Planarity :  0.005   0.068   2130
  Dihedral  :  5.216  21.721   1686
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.20 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.64 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.20), residues: 1530
  helix: -0.97 (0.44), residues: 108
  sheet: -0.59 (0.24), residues: 495
  loop : -2.53 (0.18), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 465 
 PHE   0.013   0.002   PHE A 447 
 TYR   0.023   0.002   TYR B 362 
 ARG   0.002   0.000   ARG A 590 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02923 (  264)
  hydrogen bonds       : angle       4.64742 (  702)
  covalent geometry    : bond        0.00430 (11763)
  covalent geometry    : angle       0.60159 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 1.236 
Fit side-chains
REVERT: C  498 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7401 (mp0)
REVERT: C  600 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8108 (mt-10)
  outliers start: 31
  outliers final: 28
  residues processed: 106
  average time/residue: 0.1622
  time to fit residues: 29.4038
Evaluate side-chains
  103 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  366 SER
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  498 GLU
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  561 THR
Chi-restraints excluded: chain C residue  680 MET
Chi-restraints excluded: chain C residue  703 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 133 optimal weight:    0.0010
   chunk 12 optimal weight:    0.7980
   chunk 128 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 130 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.5390

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.106070 restraints weight = 14540.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.43
r_work: 0.3263 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11763  Z= 0.145
  Angle     :  0.573   7.067  15951  Z= 0.312
  Chirality :  0.047   0.277   1767
  Planarity :  0.005   0.066   2130
  Dihedral  :  5.104  21.570   1686
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.93 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.13 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.20), residues: 1530
  helix: -0.88 (0.45), residues: 108
  sheet: -0.58 (0.25), residues: 495
  loop : -2.49 (0.18), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 465 
 PHE   0.014   0.001   PHE C 387 
 TYR   0.017   0.001   TYR B 362 
 ARG   0.002   0.000   ARG A 590 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02819 (  264)
  hydrogen bonds       : angle       4.53590 (  702)
  covalent geometry    : bond        0.00338 (11763)
  covalent geometry    : angle       0.57271 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 83
  time to evaluate  : 1.288 
Fit side-chains
REVERT: C  498 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7431 (mp0)
REVERT: C  600 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8080 (mt-10)
  outliers start: 34
  outliers final: 30
  residues processed: 111
  average time/residue: 0.1631
  time to fit residues: 30.1747
Evaluate side-chains
  111 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  680 MET
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  366 SER
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  498 GLU
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  561 THR
Chi-restraints excluded: chain C residue  680 MET
Chi-restraints excluded: chain C residue  703 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 69 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 133 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 149 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.122699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.099725 restraints weight = 14988.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.48
r_work: 0.3239 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11763  Z= 0.176
  Angle     :  0.598   7.442  15951  Z= 0.326
  Chirality :  0.048   0.267   1767
  Planarity :  0.005   0.066   2130
  Dihedral  :  5.181  21.578   1686
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.39 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.37 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.20), residues: 1530
  helix: -0.93 (0.44), residues: 108
  sheet: -0.61 (0.25), residues: 495
  loop : -2.51 (0.18), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 502 
 HIS   0.003   0.001   HIS C 476 
 PHE   0.012   0.001   PHE C 387 
 TYR   0.021   0.001   TYR B 362 
 ARG   0.002   0.000   ARG C 437 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02907 (  264)
  hydrogen bonds       : angle       4.58747 (  702)
  covalent geometry    : bond        0.00414 (11763)
  covalent geometry    : angle       0.59756 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 1.358 
Fit side-chains
REVERT: B  505 TYR cc_start: 0.8518 (t80) cc_final: 0.8302 (t80)
REVERT: C  498 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7472 (mp0)
REVERT: C  600 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8108 (mt-10)
  outliers start: 32
  outliers final: 30
  residues processed: 107
  average time/residue: 0.1634
  time to fit residues: 30.1359
Evaluate side-chains
  108 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  680 MET
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  375 THR
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  366 SER
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  498 GLU
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  561 THR
Chi-restraints excluded: chain C residue  680 MET
Chi-restraints excluded: chain C residue  703 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 137 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 134 optimal weight:    0.3980
   chunk 148 optimal weight:    0.0000
   chunk 122 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 318 ASN
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.107494 restraints weight = 14322.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.42
r_work: 0.3283 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11763  Z= 0.114
  Angle     :  0.564  10.902  15951  Z= 0.303
  Chirality :  0.046   0.255   1767
  Planarity :  0.005   0.066   2130
  Dihedral  :  4.943  20.953   1686
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.67 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.70 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.21), residues: 1530
  helix: -0.78 (0.46), residues: 108
  sheet: -0.52 (0.25), residues: 495
  loop : -2.46 (0.19), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 502 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.012   0.001   PHE B 755 
 TYR   0.025   0.001   TYR B 362 
 ARG   0.002   0.000   ARG C 437 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02713 (  264)
  hydrogen bonds       : angle       4.41539 (  702)
  covalent geometry    : bond        0.00255 (11763)
  covalent geometry    : angle       0.56378 (15951)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 1.234 
Fit side-chains
REVERT: A  725 VAL cc_start: 0.9037 (m) cc_final: 0.8817 (m)
REVERT: B  482 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8876 (p)
REVERT: C  318 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8493 (p0)
REVERT: C  498 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7415 (mp0)
REVERT: C  600 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8082 (mt-10)
  outliers start: 29
  outliers final: 26
  residues processed: 116
  average time/residue: 0.1586
  time to fit residues: 31.2049
Evaluate side-chains
  118 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  680 MET
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  386 MET
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  498 GLU
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  318 ASN
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  366 SER
Chi-restraints excluded: chain C residue  375 THR
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  498 GLU
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  561 THR
Chi-restraints excluded: chain C residue  680 MET
Chi-restraints excluded: chain C residue  703 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 97 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 121 optimal weight:    6.9990
   chunk 134 optimal weight:    4.9990
   chunk 17 optimal weight:    0.3980
   chunk 147 optimal weight:    7.9990
   chunk 116 optimal weight:    1.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 473 ASN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.129634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.107369 restraints weight = 14343.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.42
r_work: 0.3267 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.174  11763  Z= 0.243
  Angle     :  0.866  59.194  15951  Z= 0.514
  Chirality :  0.048   0.458   1767
  Planarity :  0.005   0.113   2130
  Dihedral  :  4.988  28.502   1686
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.80 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.61 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.21), residues: 1530
  helix: -0.79 (0.46), residues: 108
  sheet: -0.52 (0.25), residues: 495
  loop : -2.46 (0.19), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 502 
 HIS   0.002   0.001   HIS C 684 
 PHE   0.010   0.001   PHE B 755 
 TYR   0.024   0.001   TYR B 362 
 ARG   0.001   0.000   ARG C 437 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02738 (  264)
  hydrogen bonds       : angle       4.41638 (  702)
  covalent geometry    : bond        0.00452 (11763)
  covalent geometry    : angle       0.86582 (15951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5127.83 seconds
wall clock time: 90 minutes 20.40 seconds (5420.40 seconds total)