Starting phenix.real_space_refine
on Wed Sep 25 23:04:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/09_2024/7xy1_33507.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/09_2024/7xy1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/09_2024/7xy1_33507.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/09_2024/7xy1_33507.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/09_2024/7xy1_33507.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/09_2024/7xy1_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.79, per 1000 atoms: 0.76
  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: 3.22
  Conformation dependent library (CDL) restraints added in 1.7 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: 2.03
  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: 4.81

  Time building geometry restraints manager: 3.68 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     36.320
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.390
-------------------------------------------------------------------------------
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= 0.308
  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 

*********************** 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 fitting.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.341 
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: 0.1716
  time to fit residues: 35.1788
Evaluate side-chains
  90 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
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= 0.631
  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 

*********************** 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 fitting.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 1.649 
Fit side-chains
REVERT: A  670 CYS cc_start: 0.8314 (t) cc_final: 0.8093 (t)
REVERT: B  479 MET cc_start: 0.8209 (ttt) cc_final: 0.8003 (ttt)
REVERT: C  479 MET cc_start: 0.7923 (ttt) cc_final: 0.7706 (ttt)
REVERT: C  498 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7160 (mp0)
  outliers start: 21
  outliers final: 14
  residues processed: 93
  average time/residue: 0.2182
  time to fit residues: 31.7713
Evaluate side-chains
  81 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
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 77 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 115 optimal weight:    0.8980
   chunk 94 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 139 optimal weight:    0.3980
   chunk 150 optimal weight:    0.6980
   chunk 123 optimal weight:    0.7980
   chunk 138 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11763  Z= 0.151
  Angle     :  0.556   5.841  15951  Z= 0.304
  Chirality :  0.047   0.227   1767
  Planarity :  0.005   0.067   2130
  Dihedral  :  5.074  24.476   1689
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.89 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.08 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.07 (0.44), residues: 108
  sheet: -0.59 (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 A 502 
 HIS   0.003   0.001   HIS A 684 
 PHE   0.009   0.001   PHE C 521 
 TYR   0.020   0.001   TYR B 362 
 ARG   0.002   0.000   ARG A 770 

*********************** 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
  115 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 1.442 
Fit side-chains
REVERT: C  600 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7785 (mt-10)
  outliers start: 22
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1884
  time to fit residues: 34.4309
Evaluate side-chains
  89 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 2.230 
-------------------------------------------------------------------------------
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 137 optimal weight:    8.9990
   chunk 104 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 139 optimal weight:    2.9990
   chunk 147 optimal weight:    1.9990
   chunk 132 optimal weight:    8.9990
   chunk 39 optimal weight:   20.0000
   chunk 123 optimal weight:    3.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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**
** 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: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1658

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= 0.261
  Angle     :  0.591   8.222  15951  Z= 0.320
  Chirality :  0.048   0.329   1767
  Planarity :  0.005   0.062   2130
  Dihedral  :  5.146  21.202   1689
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.20 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.14 %
    Favored  : 85.60 %
  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: -2.46 (0.20), residues: 1530
  helix: -0.98 (0.45), residues: 108
  sheet: -0.43 (0.25), residues: 477
  loop : -2.51 (0.18), residues: 945

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   0.013   0.001   PHE A 447 
 TYR   0.018   0.001   TYR B 362 
 ARG   0.002   0.000   ARG B 590 

*********************** 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
  111 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 1.399 
Fit side-chains
REVERT: C  600 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7836 (mt-10)
  outliers start: 28
  outliers final: 25
  residues processed: 102
  average time/residue: 0.1809
  time to fit residues: 30.1164
Evaluate side-chains
  98 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
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  386 MET
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  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  356 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0050
   chunk 61 optimal weight:    6.9990
   chunk 126 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9990
   chunk 132 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    2.0002

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1765

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= 0.282
  Angle     :  0.592   6.888  15951  Z= 0.323
  Chirality :  0.048   0.283   1767
  Planarity :  0.005   0.069   2130
  Dihedral  :  5.141  21.875   1686
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.20 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.30 %
    Favored  : 84.55 %
  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: -1.02 (0.44), residues: 108
  sheet: -0.52 (0.25), residues: 480
  loop : -2.54 (0.18), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 502 
 HIS   0.003   0.001   HIS A 476 
 PHE   0.013   0.001   PHE A 447 
 TYR   0.021   0.001   TYR B 362 
 ARG   0.002   0.000   ARG A 590 

*********************** 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
  118 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 79
  time to evaluate  : 1.562 
Fit side-chains
REVERT: C  498 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7124 (mp0)
REVERT: C  600 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7684 (mt-10)
  outliers start: 39
  outliers final: 29
  residues processed: 110
  average time/residue: 0.2042
  time to fit residues: 36.5034
Evaluate side-chains
  102 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
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  386 MET
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 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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 133 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 148 optimal weight:   10.0000
   chunk 122 optimal weight:    6.9990
   chunk 68 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 77 optimal weight:    0.6980
   chunk 142 optimal weight:    0.8980
   overall best weight:    2.9186

-------------------------------------------------------------------------------
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**
A 739 GLN
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
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 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  11763  Z= 0.392
  Angle     :  0.641   7.906  15951  Z= 0.351
  Chirality :  0.050   0.288   1767
  Planarity :  0.005   0.070   2130
  Dihedral  :  5.496  23.338   1686
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.26 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.11 %
    Favored  : 83.50 %
  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: -2.65 (0.20), residues: 1530
  helix: -1.12 (0.44), residues: 108
  sheet: -0.84 (0.25), residues: 465
  loop : -2.45 (0.18), residues: 957

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 502 
 HIS   0.004   0.002   HIS A 476 
 PHE   0.016   0.002   PHE A 447 
 TYR   0.019   0.002   TYR B 362 
 ARG   0.002   0.000   ARG B 519 

*********************** 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
  113 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 71
  time to evaluate  : 1.431 
Fit side-chains
REVERT: C  498 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7182 (mp0)
  outliers start: 42
  outliers final: 32
  residues processed: 106
  average time/residue: 0.1631
  time to fit residues: 29.0848
Evaluate side-chains
  103 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 70
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
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  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 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  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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 108 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 147 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11763  Z= 0.327
  Angle     :  0.622   7.140  15951  Z= 0.341
  Chirality :  0.049   0.305   1767
  Planarity :  0.005   0.075   2130
  Dihedral  :  5.432  23.817   1686
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.72 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.32 %
    Favored  : 82.77 %
  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: -2.67 (0.20), residues: 1530
  helix: -1.14 (0.43), residues: 108
  sheet: -0.65 (0.24), residues: 492
  loop : -2.63 (0.18), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 502 
 HIS   0.004   0.001   HIS A 476 
 PHE   0.014   0.002   PHE B 755 
 TYR   0.020   0.002   TYR B 362 
 ARG   0.002   0.000   ARG B 519 

*********************** 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
  113 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 77
  time to evaluate  : 1.329 
Fit side-chains
REVERT: B  278 THR cc_start: 0.8981 (p) cc_final: 0.8773 (p)
REVERT: C  498 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7151 (mp0)
  outliers start: 36
  outliers final: 33
  residues processed: 107
  average time/residue: 0.1590
  time to fit residues: 28.9468
Evaluate side-chains
  105 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 71
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
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  386 MET
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 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  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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0670
   chunk 44 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 100 optimal weight:    7.9990
   chunk 72 optimal weight:    0.3980
   chunk 13 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 134 optimal weight:    3.9990
   chunk 141 optimal weight:    0.8980
   overall best weight:    0.6720

-------------------------------------------------------------------------------
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**
** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 471 ASN
B 494 ASN
C 318 ASN
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 494 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11763  Z= 0.144
  Angle     :  0.540   7.069  15951  Z= 0.294
  Chirality :  0.046   0.276   1767
  Planarity :  0.005   0.070   2130
  Dihedral  :  4.890  21.246   1686
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.74 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.53 %
    Favored  : 82.28 %
  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: -2.45 (0.20), residues: 1530
  helix: -0.89 (0.45), residues: 108
  sheet: -0.52 (0.25), residues: 495
  loop : -2.49 (0.18), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 502 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.013   0.001   PHE B 755 
 TYR   0.024   0.001   TYR B 362 
 ARG   0.002   0.000   ARG A 706 

*********************** 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
  124 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 1.310 
Fit side-chains
REVERT: C  318 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8396 (p0)
REVERT: C  600 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7678 (mt-10)
  outliers start: 27
  outliers final: 20
  residues processed: 121
  average time/residue: 0.1564
  time to fit residues: 32.0556
Evaluate side-chains
  102 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  386 MET
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  366 SER
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  482 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 C residue  295 VAL
Chi-restraints excluded: chain C residue  318 ASN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 128 optimal weight:    4.9990
   chunk 137 optimal weight:    0.0030
   chunk 141 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 42 optimal weight:    0.3980
   chunk 124 optimal weight:    4.9990
   chunk 129 optimal weight:    0.0070
   chunk 136 optimal weight:    0.5980
   chunk 90 optimal weight:    0.2980
   overall best weight:    0.2608

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

Flipped N/Q/H residues before XYZ refinement:
A 332 GLN
** 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 341 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 341 HIS
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11763  Z= 0.118
  Angle     :  0.530   7.711  15951  Z= 0.288
  Chirality :  0.045   0.260   1767
  Planarity :  0.004   0.067   2130
  Dihedral  :  4.584  19.490   1686
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.08 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.42 %
    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: -2.29 (0.21), residues: 1530
  helix: -0.56 (0.48), residues: 108
  sheet: -0.40 (0.25), residues: 495
  loop : -2.42 (0.18), residues: 927

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 502 
 HIS   0.005   0.001   HIS C 341 
 PHE   0.013   0.001   PHE C 387 
 TYR   0.010   0.001   TYR B 362 
 ARG   0.002   0.000   ARG C 526 

*********************** 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
  114 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 1.302 
Fit side-chains
REVERT: A  677 ASP cc_start: 0.8296 (t0) cc_final: 0.7920 (t0)
REVERT: C  318 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8224 (p0)
REVERT: C  600 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7707 (mt-10)
  outliers start: 19
  outliers final: 14
  residues processed: 111
  average time/residue: 0.1670
  time to fit residues: 30.4908
Evaluate side-chains
  102 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  366 SER
Chi-restraints excluded: chain B residue  471 ASN
Chi-restraints excluded: chain B residue  531 SER
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  318 ASN
Chi-restraints excluded: chain C residue  561 THR
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 145 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 152 optimal weight:    9.9990
   chunk 140 optimal weight:    0.0020
   chunk 121 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 93 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    2.5996

-------------------------------------------------------------------------------
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 678 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**
** B 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11763  Z= 0.356
  Angle     :  0.641  13.189  15951  Z= 0.348
  Chirality :  0.049   0.256   1767
  Planarity :  0.005   0.068   2130
  Dihedral  :  5.186  21.060   1683
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.26 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.50 %
    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: -2.45 (0.21), residues: 1530
  helix: -0.72 (0.47), residues: 108
  sheet: -0.67 (0.25), residues: 462
  loop : -2.36 (0.18), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 502 
 HIS   0.004   0.001   HIS A 476 
 PHE   0.015   0.002   PHE C 387 
 TYR   0.016   0.002   TYR C 362 
 ARG   0.002   0.000   ARG B 519 

********************** 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
  96 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 1.295 
Fit side-chains
  outliers start: 18
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1635
  time to fit residues: 25.6429
Evaluate side-chains
  93 residues out of total 1236 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain B residue  295 VAL
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  498 GLU
Chi-restraints excluded: chain B residue  531 SER
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  561 THR
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 129 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 111 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 121 optimal weight:    3.9990
   chunk 50 optimal weight:    8.9990
   chunk 124 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 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 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.107738 restraints weight = 14287.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.43
r_work: 0.3258 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1916

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= 0.172
  Angle     :  0.565  12.492  15951  Z= 0.303
  Chirality :  0.046   0.248   1767
  Planarity :  0.005   0.074   2130
  Dihedral  :  4.868  20.598   1683
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.28 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.50 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.21), residues: 1530
  helix: -0.64 (0.47), residues: 108
  sheet: -0.72 (0.24), residues: 525
  loop : -2.40 (0.19), residues: 897

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   0.013   0.001   PHE B 755 
 TYR   0.011   0.001   TYR B 523 
 ARG   0.002   0.000   ARG C 437 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2288.37 seconds
wall clock time: 42 minutes 17.06 seconds (2537.06 seconds total)