Starting phenix.real_space_refine
on Sat Sep 12 06:55:22 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d1w_7786/09_2026/6d1w_7786.map"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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      72      5.16       5
     C    9620      2.51       5
     N    2312      2.21       5
     O    2488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14492
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3581
          Classifications: {'peptide': 451}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 436}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 137
          Unresolved non-hydrogen angles: 169
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 10, 'ASP:plan': 12, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 96
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.05, per 1000 atoms: 0.21
  Number of scatterers: 14492
  At special positions: 0
  Unit cell: (110.62, 110.62, 92.3856, 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      72     16.00
     O    2488      8.00
     N    2312      7.00
     C    9620      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 344 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 344 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 331 " - pdb=" SG  CYS C 344 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D 331 " - pdb=" SG  CYS D 344 " distance=2.01

  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
  Links applied
    NAG-ASN
      " NAG A 801 " - " ASN A 328 "
      " NAG A 802 " - " ASN A 362 "
      " NAG A 803 " - " ASN A 375 "
      " NAG B 801 " - " ASN B 328 "
      " NAG B 802 " - " ASN B 362 "
      " NAG B 803 " - " ASN B 375 "
      " NAG C 801 " - " ASN C 328 "
      " NAG C 802 " - " ASN C 362 "
      " NAG C 803 " - " ASN C 375 "
      " NAG D 801 " - " ASN D 328 "
      " NAG D 802 " - " ASN D 362 "
      " NAG D 803 " - " ASN D 375 "
  Time building additional restraints: 1.16
  Conformation dependent library (CDL) restraints added in 630.5 milliseconds
  

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3456

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 12 sheets defined
      60.4% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 216 through 242
      removed outlier: 3.518A  pdb=" N   ILE A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 258
      removed outlier: 3.825A  pdb=" N   TYR A 249 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
    Processing helix  chain 'A' and resid 275 through 285
    Processing helix  chain 'A' and resid 285 through 291
      removed outlier: 3.577A  pdb=" N   ASP A 289 " --> pdb=" O   GLY A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 331
      removed outlier: 3.614A  pdb=" N   SER A 330 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   CYS A 331 " --> pdb=" O   ASN A 328 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 327 through 331'
    Processing helix  chain 'A' and resid 398 through 412
    Processing helix  chain 'A' and resid 467 through 491
      removed outlier: 3.505A  pdb=" N   ILE A 484 " --> pdb=" O   PHE A 480 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A 489 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A 490 " --> pdb=" O   TYR A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 528
      removed outlier: 3.793A  pdb=" N   VAL A 513 " --> pdb=" O   CYS A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 531
      No H-bonds generated for 'chain 'A' and resid 529 through 531'
    Processing helix  chain 'A' and resid 532 through 541
      removed outlier: 3.691A  pdb=" N   ASP A 541 " --> pdb=" O   GLN A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 572
    Processing helix  chain 'A' and resid 573 through 581
      removed outlier: 3.769A  pdb=" N   ILE A 577 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE A 579 " --> pdb=" O   LYS A 575 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ARG A 581 " --> pdb=" O   ILE A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 619
      removed outlier: 3.901A  pdb=" N   THR A 588 " --> pdb=" O   SER A 584 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   THR A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG A 592 " --> pdb=" O   THR A 588 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS A 595 " --> pdb=" O   SER A 591 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ASP A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLY A 599 " --> pdb=" O   LYS A 595 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   MET A 603 " --> pdb=" O   GLY A 599 " (cutoff:3.500A)
      Proline residue:  A 604  - end of helix
    Processing helix  chain 'A' and resid 623 through 627
    Processing helix  chain 'A' and resid 628 through 642
    Processing helix  chain 'A' and resid 645 through 653
      removed outlier: 4.009A  pdb=" N   ILE A 649 " --> pdb=" O   ASN A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 681
      removed outlier: 3.653A  pdb=" N   PHE A 669 " --> pdb=" O   VAL A 665 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN A 674 " --> pdb=" O   PHE A 670 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 677 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 242
      removed outlier: 3.518A  pdb=" N   ILE B 232 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 258
      removed outlier: 3.824A  pdb=" N   TYR B 249 " --> pdb=" O   ASN B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 273
    Processing helix  chain 'B' and resid 275 through 285
    Processing helix  chain 'B' and resid 285 through 291
      removed outlier: 3.578A  pdb=" N   ASP B 289 " --> pdb=" O   GLY B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 331
      removed outlier: 3.615A  pdb=" N   SER B 330 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   CYS B 331 " --> pdb=" O   ASN B 328 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 327 through 331'
    Processing helix  chain 'B' and resid 398 through 412
    Processing helix  chain 'B' and resid 467 through 491
      removed outlier: 3.505A  pdb=" N   ILE B 484 " --> pdb=" O   PHE B 480 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL B 489 " --> pdb=" O   PHE B 485 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU B 490 " --> pdb=" O   TYR B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 528
      removed outlier: 3.793A  pdb=" N   VAL B 513 " --> pdb=" O   CYS B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 531
      No H-bonds generated for 'chain 'B' and resid 529 through 531'
    Processing helix  chain 'B' and resid 532 through 541
      removed outlier: 3.691A  pdb=" N   ASP B 541 " --> pdb=" O   GLN B 537 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 572
    Processing helix  chain 'B' and resid 573 through 581
      removed outlier: 3.768A  pdb=" N   ILE B 577 " --> pdb=" O   LEU B 573 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   PHE B 579 " --> pdb=" O   LYS B 575 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ARG B 581 " --> pdb=" O   ILE B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 619
      removed outlier: 3.902A  pdb=" N   THR B 588 " --> pdb=" O   SER B 584 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   THR B 589 " --> pdb=" O   GLN B 585 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ARG B 592 " --> pdb=" O   THR B 588 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS B 595 " --> pdb=" O   SER B 591 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ASP B 596 " --> pdb=" O   ARG B 592 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE B 598 " --> pdb=" O   ALA B 594 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLY B 599 " --> pdb=" O   LYS B 595 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   MET B 603 " --> pdb=" O   GLY B 599 " (cutoff:3.500A)
      Proline residue:  B 604  - end of helix
    Processing helix  chain 'B' and resid 623 through 627
    Processing helix  chain 'B' and resid 628 through 642
    Processing helix  chain 'B' and resid 645 through 653
      removed outlier: 4.009A  pdb=" N   ILE B 649 " --> pdb=" O   ASN B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 681
      removed outlier: 3.652A  pdb=" N   PHE B 669 " --> pdb=" O   VAL B 665 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN B 674 " --> pdb=" O   PHE B 670 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU B 677 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 242
      removed outlier: 3.519A  pdb=" N   ILE C 232 " --> pdb=" O   LEU C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 258
      removed outlier: 3.825A  pdb=" N   TYR C 249 " --> pdb=" O   ASN C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 273
    Processing helix  chain 'C' and resid 275 through 285
    Processing helix  chain 'C' and resid 285 through 291
      removed outlier: 3.578A  pdb=" N   ASP C 289 " --> pdb=" O   GLY C 285 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 331
      removed outlier: 3.615A  pdb=" N   SER C 330 " --> pdb=" O   ARG C 327 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   CYS C 331 " --> pdb=" O   ASN C 328 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 327 through 331'
    Processing helix  chain 'C' and resid 398 through 412
    Processing helix  chain 'C' and resid 467 through 491
      removed outlier: 3.505A  pdb=" N   ILE C 484 " --> pdb=" O   PHE C 480 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL C 489 " --> pdb=" O   PHE C 485 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU C 490 " --> pdb=" O   TYR C 486 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 505 through 528
      removed outlier: 3.793A  pdb=" N   VAL C 513 " --> pdb=" O   CYS C 509 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 529 through 531
      No H-bonds generated for 'chain 'C' and resid 529 through 531'
    Processing helix  chain 'C' and resid 532 through 541
      removed outlier: 3.692A  pdb=" N   ASP C 541 " --> pdb=" O   GLN C 537 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 548 through 572
    Processing helix  chain 'C' and resid 573 through 581
      removed outlier: 3.769A  pdb=" N   ILE C 577 " --> pdb=" O   LEU C 573 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   PHE C 579 " --> pdb=" O   LYS C 575 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ARG C 581 " --> pdb=" O   ILE C 577 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 583 through 619
      removed outlier: 3.901A  pdb=" N   THR C 588 " --> pdb=" O   SER C 584 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   THR C 589 " --> pdb=" O   GLN C 585 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG C 592 " --> pdb=" O   THR C 588 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS C 595 " --> pdb=" O   SER C 591 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ASP C 596 " --> pdb=" O   ARG C 592 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE C 598 " --> pdb=" O   ALA C 594 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLY C 599 " --> pdb=" O   LYS C 595 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   MET C 603 " --> pdb=" O   GLY C 599 " (cutoff:3.500A)
      Proline residue:  C 604  - end of helix
    Processing helix  chain 'C' and resid 623 through 627
    Processing helix  chain 'C' and resid 628 through 642
    Processing helix  chain 'C' and resid 645 through 653
      removed outlier: 4.010A  pdb=" N   ILE C 649 " --> pdb=" O   ASN C 645 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 655 through 681
      removed outlier: 3.652A  pdb=" N   PHE C 669 " --> pdb=" O   VAL C 665 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN C 674 " --> pdb=" O   PHE C 670 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU C 677 " --> pdb=" O   LEU C 673 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 217 through 242
      removed outlier: 3.519A  pdb=" N   ILE D 232 " --> pdb=" O   LEU D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 258
      removed outlier: 3.826A  pdb=" N   TYR D 249 " --> pdb=" O   ASN D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 273
    Processing helix  chain 'D' and resid 275 through 285
    Processing helix  chain 'D' and resid 285 through 291
      removed outlier: 3.578A  pdb=" N   ASP D 289 " --> pdb=" O   GLY D 285 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 331
      removed outlier: 3.614A  pdb=" N   SER D 330 " --> pdb=" O   ARG D 327 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   CYS D 331 " --> pdb=" O   ASN D 328 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 327 through 331'
    Processing helix  chain 'D' and resid 398 through 412
    Processing helix  chain 'D' and resid 467 through 491
      removed outlier: 3.505A  pdb=" N   ILE D 484 " --> pdb=" O   PHE D 480 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL D 489 " --> pdb=" O   PHE D 485 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU D 490 " --> pdb=" O   TYR D 486 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 505 through 528
      removed outlier: 3.793A  pdb=" N   VAL D 513 " --> pdb=" O   CYS D 509 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 529 through 531
      No H-bonds generated for 'chain 'D' and resid 529 through 531'
    Processing helix  chain 'D' and resid 532 through 541
      removed outlier: 3.691A  pdb=" N   ASP D 541 " --> pdb=" O   GLN D 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 572
    Processing helix  chain 'D' and resid 573 through 581
      removed outlier: 3.769A  pdb=" N   ILE D 577 " --> pdb=" O   LEU D 573 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   PHE D 579 " --> pdb=" O   LYS D 575 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ARG D 581 " --> pdb=" O   ILE D 577 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 583 through 619
      removed outlier: 3.901A  pdb=" N   THR D 588 " --> pdb=" O   SER D 584 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   THR D 589 " --> pdb=" O   GLN D 585 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG D 592 " --> pdb=" O   THR D 588 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS D 595 " --> pdb=" O   SER D 591 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ASP D 596 " --> pdb=" O   ARG D 592 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE D 598 " --> pdb=" O   ALA D 594 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLY D 599 " --> pdb=" O   LYS D 595 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   MET D 603 " --> pdb=" O   GLY D 599 " (cutoff:3.500A)
      Proline residue:  D 604  - end of helix
    Processing helix  chain 'D' and resid 623 through 627
    Processing helix  chain 'D' and resid 628 through 642
    Processing helix  chain 'D' and resid 645 through 653
      removed outlier: 4.009A  pdb=" N   ILE D 649 " --> pdb=" O   ASN D 645 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 655 through 681
      removed outlier: 3.653A  pdb=" N   PHE D 669 " --> pdb=" O   VAL D 665 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN D 674 " --> pdb=" O   PHE D 670 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU D 677 " --> pdb=" O   LEU D 673 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309
    Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309
      removed outlier: 6.310A  pdb=" N   LEU A 316 " --> pdb=" O   TYR A 429 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   TYR A 429 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   VAL A 318 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
      removed outlier: 5.784A  pdb=" N   SER A 427 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 435 " --> pdb=" O   ASN A 430 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380
    Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309
    Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309
      removed outlier: 6.310A  pdb=" N   LEU B 316 " --> pdb=" O   TYR B 429 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   TYR B 429 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   VAL B 318 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   SER B 427 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B 435 " --> pdb=" O   ASN B 430 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380
    Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309
    Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309
      removed outlier: 6.309A  pdb=" N   LEU C 316 " --> pdb=" O   TYR C 429 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   TYR C 429 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   VAL C 318 " --> pdb=" O   SER C 427 " (cutoff:3.500A)
      removed outlier: 5.784A  pdb=" N   SER C 427 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU C 435 " --> pdb=" O   ASN C 430 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380
    Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309
    Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309
      removed outlier: 6.309A  pdb=" N   LEU D 316 " --> pdb=" O   TYR D 429 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   TYR D 429 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   VAL D 318 " --> pdb=" O   SER D 427 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   SER D 427 " --> pdb=" O   VAL D 318 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU D 435 " --> pdb=" O   ASN D 430 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380

    837 hydrogen bonds defined for protein.
    2403 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.84

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 2136
        1.28 -     1.41: 4296
        1.41 -     1.54: 8324
        1.54 -     1.68: 12
        1.68 -     1.81: 108
  Bond restraints: 14876
  Sorted by residual:
  bond pdb=" C   ALA C 356 "
       pdb=" N   PRO C 357 "
    ideal  model  delta    sigma   weight residual
    1.334  1.145  0.189 2.34e-02 1.83e+03 6.54e+01
  bond pdb=" C   ALA D 356 "
       pdb=" N   PRO D 357 "
    ideal  model  delta    sigma   weight residual
    1.334  1.145  0.189 2.34e-02 1.83e+03 6.49e+01
  bond pdb=" C   ALA A 356 "
       pdb=" N   PRO A 357 "
    ideal  model  delta    sigma   weight residual
    1.334  1.145  0.189 2.34e-02 1.83e+03 6.49e+01
  bond pdb=" C   ALA B 356 "
       pdb=" N   PRO B 357 "
    ideal  model  delta    sigma   weight residual
    1.334  1.145  0.188 2.34e-02 1.83e+03 6.49e+01
  bond pdb=" CA  ALA D 303 "
       pdb=" C   ALA D 303 "
    ideal  model  delta    sigma   weight residual
    1.524  1.550 -0.026 1.29e-02 6.01e+03 4.13e+00
  ... (remaining 14871 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 19579
        1.85 -     3.70: 560
        3.70 -     5.55: 85
        5.55 -     7.40: 32
        7.40 -     9.25: 4
  Bond angle restraints: 20260
  Sorted by residual:
  angle pdb=" N   ALA B 303 "
        pdb=" CA  ALA B 303 "
        pdb=" C   ALA B 303 "
      ideal   model   delta    sigma   weight residual
     111.36  118.10   -6.74 1.09e+00 8.42e-01 3.83e+01
  angle pdb=" N   ALA C 303 "
        pdb=" CA  ALA C 303 "
        pdb=" C   ALA C 303 "
      ideal   model   delta    sigma   weight residual
     111.36  118.08   -6.72 1.09e+00 8.42e-01 3.80e+01
  angle pdb=" N   ALA A 303 "
        pdb=" CA  ALA A 303 "
        pdb=" C   ALA A 303 "
      ideal   model   delta    sigma   weight residual
     111.36  118.05   -6.69 1.09e+00 8.42e-01 3.77e+01
  angle pdb=" N   ALA D 303 "
        pdb=" CA  ALA D 303 "
        pdb=" C   ALA D 303 "
      ideal   model   delta    sigma   weight residual
     111.36  118.03   -6.67 1.09e+00 8.42e-01 3.75e+01
  angle pdb=" C   LYS D 294 "
        pdb=" N   MET D 295 "
        pdb=" CA  MET D 295 "
      ideal   model   delta    sigma   weight residual
     121.70  128.13   -6.43 1.80e+00 3.09e-01 1.28e+01
  ... (remaining 20255 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 8224
       16.03 -    32.07: 136
       32.07 -    48.10: 48
       48.10 -    64.13: 0
       64.13 -    80.16: 12
  Dihedral angle restraints: 8420
    sinusoidal: 3084
      harmonic: 5336
  Sorted by residual:
  dihedral pdb=" CA  ILE A 644 "
           pdb=" C   ILE A 644 "
           pdb=" N   ASN A 645 "
           pdb=" CA  ASN A 645 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ILE D 644 "
           pdb=" C   ILE D 644 "
           pdb=" N   ASN D 645 "
           pdb=" CA  ASN D 645 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ILE C 644 "
           pdb=" C   ILE C 644 "
           pdb=" N   ASN C 645 "
           pdb=" CA  ASN C 645 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.14   24.86     0      5.00e+00 4.00e-02 2.47e+01
  ... (remaining 8417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1342
       0.030 -    0.059: 636
       0.059 -    0.089: 251
       0.089 -    0.118: 123
       0.118 -    0.148: 16
  Chirality restraints: 2368
  Sorted by residual:
  chirality pdb=" CA  ILE C 644 "
            pdb=" N   ILE C 644 "
            pdb=" C   ILE C 644 "
            pdb=" CB  ILE C 644 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CA  ILE A 644 "
            pdb=" N   ILE A 644 "
            pdb=" C   ILE A 644 "
            pdb=" CB  ILE A 644 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.32e-01
  chirality pdb=" CA  ILE D 644 "
            pdb=" N   ILE D 644 "
            pdb=" C   ILE D 644 "
            pdb=" CB  ILE D 644 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.16e-01
  ... (remaining 2365 not shown)

  Planarity restraints: 2496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 458 "   -0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO A 459 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 459 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 459 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 458 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO B 459 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 459 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 459 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 458 "   -0.030 5.00e-02 4.00e+02   4.57e-02 3.34e+00
        pdb=" N   PRO D 459 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO D 459 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 459 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 2493 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 550
        2.70 -     3.25: 17063
        3.25 -     3.80: 25388
        3.80 -     4.35: 30939
        4.35 -     4.90: 49131
  Nonbonded interactions: 123071
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 562 "
            pdb=" OG1 THR B 565 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" O   ALA C 562 "
            pdb=" OG1 THR C 565 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" O   ALA D 562 "
            pdb=" OG1 THR D 565 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" O   ALA A 562 "
            pdb=" OG1 THR A 565 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" OH  TYR C 227 "
            pdb=" O   VAL C 569 "
     model   vdw
     2.181 3.040
  ... (remaining 123066 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.000
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
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      :  0.007   0.189  14892  Z= 0.360
  Angle     :  0.814  12.821  20304  Z= 0.450
  Chirality :  0.043   0.148   2368
  Planarity :  0.004   0.046   2484
  Dihedral  :  8.578  80.164   4952
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 18.64
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.52 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.82 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.21 (0.16), residues: 1780
  helix: -3.02 (0.11), residues: 884
  sheet:  0.77 (0.34), residues: 184
  loop : -1.48 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 654 
 TYR   0.014   0.002   TYR C 527 
 PHE   0.014   0.002   PHE B 436 
 TRP   0.025   0.003   TRP B 380 
 HIS   0.002   0.001   HIS A 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00746 /  0.36 (14876)
  covalent geometry    : angle       0.77192 /  0.44 (20260)
  SS BOND              : bond        0.01621 /  0.81 (    4)
  SS BOND              : angle       1.99287 /  1.15 (    8)
  hydrogen bonds       : bond        0.29263 / 19.33 (  829)
  hydrogen bonds       : angle       8.77863 /  6.17 ( 2403)
  link_NAG-ASN         : bond        0.00478 /  0.33 (   12)
  link_NAG-ASN         : angle       6.13889 /  5.29 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  429 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 425
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8485 (t80) cc_final: 0.7821 (t80)
REVERT: A  590 MET cc_start: 0.5614 (mmm) cc_final: 0.5023 (mmt)
REVERT: A  616 TYR cc_start: 0.8618 (t80) cc_final: 0.8320 (t80)
REVERT: B  249 TYR cc_start: 0.8492 (t80) cc_final: 0.7809 (t80)
REVERT: B  590 MET cc_start: 0.5647 (mmm) cc_final: 0.4924 (mmt)
REVERT: B  616 TYR cc_start: 0.8644 (t80) cc_final: 0.8399 (t80)
REVERT: B  654 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8158 (mtm-85)
REVERT: C  249 TYR cc_start: 0.8504 (t80) cc_final: 0.7841 (t80)
REVERT: C  616 TYR cc_start: 0.8658 (t80) cc_final: 0.8377 (t80)
REVERT: D  249 TYR cc_start: 0.8504 (t80) cc_final: 0.7829 (t80)
REVERT: D  570 TRP cc_start: 0.8349 (m100) cc_final: 0.8142 (m100)
REVERT: D  616 TYR cc_start: 0.8616 (t80) cc_final: 0.8355 (t80)
  outliers start: 4
  outliers final: 4
  residues processed: 425
  average time/residue: 0.1099
  time to fit residues: 70.4841
Evaluate side-chains
  218 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 214
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain C residue  510 LEU
Chi-restraints excluded: chain D residue  510 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    0.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 323 GLN
A 458 GLN
A 543 ASN
A 636 GLN
A 645 ASN
B 323 GLN
B 458 GLN
B 543 ASN
B 636 GLN
C 323 GLN
C 458 GLN
C 543 ASN
C 636 GLN
C 645 ASN
D 323 GLN
D 458 GLN
D 543 ASN
D 636 GLN
D 645 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.135556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.103602 restraints weight = 24482.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.107649 restraints weight = 12620.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.110352 restraints weight = 8505.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.112072 restraints weight = 6636.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.112871 restraints weight = 5666.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14892  Z= 0.167
  Angle     :  0.660   7.392  20304  Z= 0.362
  Chirality :  0.043   0.145   2368
  Planarity :  0.005   0.046   2484
  Dihedral  :  5.748  59.338   1976
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.64 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.51 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.18), residues: 1780
  helix:  0.25 (0.15), residues: 1000
  sheet:  0.61 (0.34), residues: 176
  loop : -1.20 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 654 
 TYR   0.021   0.002   TYR C 247 
 PHE   0.028   0.002   PHE D 472 
 TRP   0.017   0.002   TRP B 380 
 HIS   0.001   0.000   HIS C 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.17 (14876)
  covalent geometry    : angle       0.64479 /  0.36 (20260)
  SS BOND              : bond        0.00022 /  0.01 (    4)
  SS BOND              : angle       1.03652 /  0.60 (    8)
  hydrogen bonds       : bond        0.05562 /  3.70 (  829)
  hydrogen bonds       : angle       5.28368 /  3.75 ( 2403)
  link_NAG-ASN         : bond        0.00376 /  0.26 (   12)
  link_NAG-ASN         : angle       3.37633 /  2.91 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 276
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 TYR cc_start: 0.8637 (t80) cc_final: 0.7718 (t80)
REVERT: A  583 MET cc_start: 0.5269 (ttt) cc_final: 0.5028 (tmm)
REVERT: A  592 ARG cc_start: 0.7333 (tpt170) cc_final: 0.6857 (ttp80)
REVERT: B  249 TYR cc_start: 0.8602 (t80) cc_final: 0.7685 (t80)
REVERT: B  487 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8299 (t80)
REVERT: B  555 GLN cc_start: 0.8377 (tt0) cc_final: 0.7952 (tm-30)
REVERT: B  583 MET cc_start: 0.5253 (ttt) cc_final: 0.5042 (tmm)
REVERT: B  592 ARG cc_start: 0.7383 (tpt170) cc_final: 0.6908 (ttp80)
REVERT: C  249 TYR cc_start: 0.8656 (t80) cc_final: 0.7782 (t80)
REVERT: C  346 ASP cc_start: 0.8144 (t0) cc_final: 0.7943 (t0)
REVERT: C  512 VAL cc_start: 0.9470 (t) cc_final: 0.9246 (p)
REVERT: C  592 ARG cc_start: 0.7399 (tpt170) cc_final: 0.6919 (ttp80)
REVERT: C  598 PHE cc_start: 0.6907 (t80) cc_final: 0.6605 (m-10)
REVERT: C  603 MET cc_start: 0.7672 (ttm) cc_final: 0.7368 (ttm)
REVERT: C  616 TYR cc_start: 0.8890 (t80) cc_final: 0.8675 (t80)
REVERT: D  249 TYR cc_start: 0.8627 (t80) cc_final: 0.7791 (t80)
REVERT: D  512 VAL cc_start: 0.9462 (t) cc_final: 0.9226 (p)
REVERT: D  570 TRP cc_start: 0.8711 (m100) cc_final: 0.8230 (m100)
REVERT: D  603 MET cc_start: 0.7664 (ttm) cc_final: 0.7347 (ttm)
  outliers start: 32
  outliers final: 19
  residues processed: 297
  average time/residue: 0.1089
  time to fit residues: 48.3698
Evaluate side-chains
  233 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 213
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  547 ASN
Chi-restraints excluded: chain A residue  631 GLU
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  547 ASN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  631 GLU
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  547 ASN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  631 GLU
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  547 ASN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  631 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 132 optimal weight:    0.6980
   chunk 176 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 154 optimal weight:    7.9990
   chunk 130 optimal weight:    0.6980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 434 ASN
A 578 ASN
B 434 ASN
B 578 ASN
C 434 ASN
C 542 GLN
C 578 ASN
D 434 ASN
D 542 GLN
D 578 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.100346 restraints weight = 24890.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104307 restraints weight = 12559.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.106982 restraints weight = 8432.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.108670 restraints weight = 6625.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.109572 restraints weight = 5711.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  14892  Z= 0.155
  Angle     :  0.601   7.306  20304  Z= 0.324
  Chirality :  0.042   0.130   2368
  Planarity :  0.004   0.052   2484
  Dihedral  :  4.630  28.973   1968
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.70 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.28 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.19), residues: 1780
  helix:  1.00 (0.16), residues: 992
  sheet:  0.24 (0.33), residues: 176
  loop : -0.94 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 464 
 TYR   0.020   0.002   TYR C 247 
 PHE   0.015   0.001   PHE D 472 
 TRP   0.011   0.001   TRP C 380 
 HIS   0.000   0.000   HIS C 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.16 (14876)
  covalent geometry    : angle       0.59202 /  0.32 (20260)
  SS BOND              : bond        0.00077 /  0.04 (    4)
  SS BOND              : angle       0.94322 /  0.55 (    8)
  hydrogen bonds       : bond        0.04412 /  2.93 (  829)
  hydrogen bonds       : angle       4.78302 /  3.39 ( 2403)
  link_NAG-ASN         : bond        0.00287 /  0.20 (   12)
  link_NAG-ASN         : angle       2.55787 /  2.20 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 247
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 TYR cc_start: 0.8603 (t80) cc_final: 0.7612 (t80)
REVERT: A  272 THR cc_start: 0.8374 (m) cc_final: 0.7763 (p)
REVERT: A  518 SER cc_start: 0.9359 (m) cc_final: 0.9031 (p)
REVERT: A  555 GLN cc_start: 0.8331 (tt0) cc_final: 0.8013 (tm-30)
REVERT: B  249 TYR cc_start: 0.8611 (t80) cc_final: 0.7754 (t80)
REVERT: B  487 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8526 (t80)
REVERT: B  518 SER cc_start: 0.9356 (m) cc_final: 0.9039 (p)
REVERT: B  555 GLN cc_start: 0.8333 (tt0) cc_final: 0.8011 (tm-30)
REVERT: B  570 TRP cc_start: 0.8654 (m100) cc_final: 0.8450 (m100)
REVERT: B  592 ARG cc_start: 0.7363 (tpt170) cc_final: 0.6838 (ttp80)
REVERT: B  598 PHE cc_start: 0.6589 (t80) cc_final: 0.6323 (m-10)
REVERT: C  249 TYR cc_start: 0.8637 (t80) cc_final: 0.7732 (t80)
REVERT: C  272 THR cc_start: 0.8309 (m) cc_final: 0.7656 (p)
REVERT: C  346 ASP cc_start: 0.8306 (t0) cc_final: 0.8003 (t0)
REVERT: C  518 SER cc_start: 0.9355 (m) cc_final: 0.9021 (p)
REVERT: C  555 GLN cc_start: 0.8397 (tt0) cc_final: 0.7916 (tm-30)
REVERT: C  583 MET cc_start: 0.6308 (tmm) cc_final: 0.5926 (ttt)
REVERT: C  592 ARG cc_start: 0.7337 (tpt170) cc_final: 0.6783 (ttp80)
REVERT: C  616 TYR cc_start: 0.8976 (t80) cc_final: 0.8726 (t80)
REVERT: D  249 TYR cc_start: 0.8609 (t80) cc_final: 0.7684 (t80)
REVERT: D  272 THR cc_start: 0.8368 (m) cc_final: 0.7746 (p)
REVERT: D  518 SER cc_start: 0.9354 (m) cc_final: 0.9026 (p)
REVERT: D  555 GLN cc_start: 0.8378 (tt0) cc_final: 0.8060 (tm-30)
  outliers start: 34
  outliers final: 25
  residues processed: 279
  average time/residue: 0.0920
  time to fit residues: 40.4557
Evaluate side-chains
  245 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 219
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  434 ASN
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  434 ASN
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  434 ASN
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  607 ILE
Chi-restraints excluded: chain D residue  640 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 165 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9980
   chunk 90 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0070
   chunk 88 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 133 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0270
   overall best weight:    0.5456

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 434 ASN
A 550 HIS
B 434 ASN
B 550 HIS
C 434 ASN
C 542 GLN
C 550 HIS
D 434 ASN
D 542 GLN
D 550 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.134651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.102220 restraints weight = 24802.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.106300 restraints weight = 12194.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109034 restraints weight = 8090.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.110741 restraints weight = 6311.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.111801 restraints weight = 5436.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  14892  Z= 0.115
  Angle     :  0.544   7.299  20304  Z= 0.294
  Chirality :  0.040   0.127   2368
  Planarity :  0.004   0.048   2484
  Dihedral  :  4.376  27.109   1968
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.25 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.18 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.19), residues: 1780
  helix:  1.46 (0.16), residues: 972
  sheet: -0.07 (0.33), residues: 176
  loop : -1.04 (0.23), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 464 
 TYR   0.018   0.001   TYR C 247 
 PHE   0.019   0.001   PHE C 670 
 TRP   0.009   0.001   TRP D 507 
 HIS   0.001   0.000   HIS C 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.12 (14876)
  covalent geometry    : angle       0.53732 /  0.29 (20260)
  SS BOND              : bond        0.00128 /  0.06 (    4)
  SS BOND              : angle       0.69744 /  0.40 (    8)
  hydrogen bonds       : bond        0.03735 /  2.48 (  829)
  hydrogen bonds       : angle       4.49597 /  3.19 ( 2403)
  link_NAG-ASN         : bond        0.00265 /  0.18 (   12)
  link_NAG-ASN         : angle       2.04667 /  1.75 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 259
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 SER cc_start: 0.9383 (m) cc_final: 0.9105 (p)
REVERT: A  600 PHE cc_start: 0.6177 (m-80) cc_final: 0.5532 (m-80)
REVERT: A  616 TYR cc_start: 0.8789 (t80) cc_final: 0.8579 (t80)
REVERT: B  249 TYR cc_start: 0.8493 (t80) cc_final: 0.7629 (t80)
REVERT: B  487 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8691 (t80)
REVERT: B  570 TRP cc_start: 0.8676 (m100) cc_final: 0.8445 (m100)
REVERT: B  592 ARG cc_start: 0.7373 (tpt170) cc_final: 0.6843 (ttp80)
REVERT: B  600 PHE cc_start: 0.6494 (m-80) cc_final: 0.5935 (m-80)
REVERT: C  249 TYR cc_start: 0.8507 (t80) cc_final: 0.7596 (t80)
REVERT: C  518 SER cc_start: 0.9384 (m) cc_final: 0.9096 (p)
REVERT: D  249 TYR cc_start: 0.8483 (t80) cc_final: 0.7470 (t80)
REVERT: D  438 VAL cc_start: 0.8858 (t) cc_final: 0.8607 (m)
REVERT: D  518 SER cc_start: 0.9384 (m) cc_final: 0.9093 (p)
REVERT: D  600 PHE cc_start: 0.6155 (m-80) cc_final: 0.5359 (m-10)
  outliers start: 39
  outliers final: 22
  residues processed: 286
  average time/residue: 0.0933
  time to fit residues: 42.1619
Evaluate side-chains
  236 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  547 ASN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  547 ASN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9990
   chunk 128 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 126 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9990
   chunk 157 optimal weight:    0.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 434 ASN
A 550 HIS
B 434 ASN
B 550 HIS
C 434 ASN
C 508 ASN
C 550 HIS
D 434 ASN
D 550 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.130980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.098803 restraints weight = 24891.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.102656 restraints weight = 12239.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.105221 restraints weight = 8126.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.106761 restraints weight = 6371.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.107812 restraints weight = 5524.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14892  Z= 0.150
  Angle     :  0.559   7.274  20304  Z= 0.298
  Chirality :  0.040   0.127   2368
  Planarity :  0.004   0.046   2484
  Dihedral  :  4.388  27.327   1968
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.43 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.20 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.19), residues: 1780
  helix:  1.27 (0.16), residues: 1000
  sheet: -0.32 (0.35), residues: 184
  loop : -0.91 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.019   0.001   TYR C 247 
 PHE   0.023   0.001   PHE C 670 
 TRP   0.014   0.001   TRP B 507 
 HIS   0.001   0.000   HIS C 379 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 (14876)
  covalent geometry    : angle       0.55374 /  0.30 (20260)
  SS BOND              : bond        0.00062 /  0.03 (    4)
  SS BOND              : angle       0.78770 /  0.46 (    8)
  hydrogen bonds       : bond        0.03708 /  2.47 (  829)
  hydrogen bonds       : angle       4.46449 /  3.17 ( 2403)
  link_NAG-ASN         : bond        0.00202 /  0.14 (   12)
  link_NAG-ASN         : angle       1.80279 /  1.52 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 234
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  600 PHE cc_start: 0.6208 (m-80) cc_final: 0.5642 (m-80)
REVERT: A  616 TYR cc_start: 0.8955 (t80) cc_final: 0.8622 (t80)
REVERT: B  487 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8715 (t80)
REVERT: B  570 TRP cc_start: 0.8703 (m100) cc_final: 0.8495 (m100)
REVERT: B  583 MET cc_start: 0.6392 (tmm) cc_final: 0.5703 (ttt)
REVERT: B  592 ARG cc_start: 0.7433 (tpt170) cc_final: 0.7158 (ptm-80)
REVERT: B  600 PHE cc_start: 0.6487 (m-80) cc_final: 0.6024 (m-80)
REVERT: C  249 TYR cc_start: 0.8552 (t80) cc_final: 0.7346 (t80)
REVERT: D  600 PHE cc_start: 0.6153 (m-80) cc_final: 0.5652 (m-80)
  outliers start: 45
  outliers final: 33
  residues processed: 262
  average time/residue: 0.0954
  time to fit residues: 39.3648
Evaluate side-chains
  245 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 211
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  434 ASN
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain C residue  278 ASP
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  434 ASN
Chi-restraints excluded: chain C residue  483 PHE
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  434 ASN
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  607 ILE
Chi-restraints excluded: chain D residue  640 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 173 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 80 optimal weight:   30.0000
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0980
   chunk 136 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9980
   chunk 168 optimal weight:    3.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 434 ASN
C 434 ASN
D 434 ASN
D 508 ASN
D 550 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.132175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.100277 restraints weight = 24717.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.104159 restraints weight = 12188.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.106967 restraints weight = 8066.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.107769 restraints weight = 6282.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108928 restraints weight = 5728.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.5163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  14892  Z= 0.129
  Angle     :  0.535   7.275  20304  Z= 0.286
  Chirality :  0.040   0.167   2368
  Planarity :  0.004   0.044   2484
  Dihedral  :  4.292  26.840   1968
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.09 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 15.69 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.19), residues: 1780
  helix:  1.28 (0.16), residues: 1000
  sheet: -0.18 (0.35), residues: 176
  loop : -0.90 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 464 
 TYR   0.019   0.001   TYR C 247 
 PHE   0.021   0.001   PHE A 670 
 TRP   0.012   0.001   TRP C 570 
 HIS   0.001   0.000   HIS D 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 (14876)
  covalent geometry    : angle       0.53052 /  0.29 (20260)
  SS BOND              : bond        0.00079 /  0.04 (    4)
  SS BOND              : angle       0.61340 /  0.35 (    8)
  hydrogen bonds       : bond        0.03503 /  2.32 (  829)
  hydrogen bonds       : angle       4.35680 /  3.10 ( 2403)
  link_NAG-ASN         : bond        0.00188 /  0.13 (   12)
  link_NAG-ASN         : angle       1.64541 /  1.39 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 226
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 THR cc_start: 0.8351 (m) cc_final: 0.7681 (p)
REVERT: A  413 VAL cc_start: 0.8315 (t) cc_final: 0.7922 (p)
REVERT: A  616 TYR cc_start: 0.8958 (t80) cc_final: 0.8635 (t80)
REVERT: B  272 THR cc_start: 0.8307 (m) cc_final: 0.7660 (p)
REVERT: B  413 VAL cc_start: 0.8328 (t) cc_final: 0.7935 (p)
REVERT: B  487 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8756 (t80)
REVERT: B  570 TRP cc_start: 0.8678 (m100) cc_final: 0.8459 (m100)
REVERT: B  600 PHE cc_start: 0.6521 (m-80) cc_final: 0.6029 (m-80)
REVERT: C  272 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7718 (p)
REVERT: C  413 VAL cc_start: 0.8328 (t) cc_final: 0.7927 (p)
REVERT: D  272 THR cc_start: 0.8364 (m) cc_final: 0.7681 (p)
REVERT: D  413 VAL cc_start: 0.8329 (t) cc_final: 0.7935 (p)
REVERT: D  600 PHE cc_start: 0.6257 (m-80) cc_final: 0.5835 (m-80)
REVERT: D  668 MET cc_start: 0.8865 (mmp) cc_final: 0.8584 (mmp)
  outliers start: 39
  outliers final: 27
  residues processed: 253
  average time/residue: 0.0932
  time to fit residues: 37.4190
Evaluate side-chains
  239 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 210
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Chi-restraints excluded: chain D residue  673 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 150 optimal weight:    0.4980
   chunk 117 optimal weight:    1.9990
   chunk 178 optimal weight:    1.9990
   chunk 133 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 73 optimal weight:    0.6980
   chunk 153 optimal weight:    0.6980
   chunk 127 optimal weight:    0.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 508 ASN
A 550 HIS
B 550 HIS
C 550 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.132879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.100598 restraints weight = 24563.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.104504 restraints weight = 12001.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.107095 restraints weight = 7988.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108658 restraints weight = 6292.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.109691 restraints weight = 5475.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  14892  Z= 0.126
  Angle     :  0.530   7.279  20304  Z= 0.283
  Chirality :  0.041   0.207   2368
  Planarity :  0.004   0.043   2484
  Dihedral  :  4.245  27.101   1968
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.48 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.92 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.19), residues: 1780
  helix:  1.34 (0.16), residues: 1000
  sheet: -0.29 (0.36), residues: 176
  loop : -0.85 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 464 
 TYR   0.019   0.001   TYR C 247 
 PHE   0.022   0.001   PHE D 670 
 TRP   0.015   0.001   TRP A 570 
 HIS   0.001   0.000   HIS C 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 (14876)
  covalent geometry    : angle       0.52630 /  0.28 (20260)
  SS BOND              : bond        0.00089 /  0.04 (    4)
  SS BOND              : angle       0.66569 /  0.39 (    8)
  hydrogen bonds       : bond        0.03436 /  2.27 (  829)
  hydrogen bonds       : angle       4.30248 /  3.06 ( 2403)
  link_NAG-ASN         : bond        0.00183 /  0.13 (   12)
  link_NAG-ASN         : angle       1.47001 /  1.23 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 225
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ILE cc_start: 0.9031 (mm) cc_final: 0.8828 (mm)
REVERT: A  272 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.7804 (p)
REVERT: A  413 VAL cc_start: 0.8257 (t) cc_final: 0.7834 (p)
REVERT: A  616 TYR cc_start: 0.9004 (t80) cc_final: 0.8672 (t80)
REVERT: B  272 THR cc_start: 0.8343 (m) cc_final: 0.7702 (p)
REVERT: B  413 VAL cc_start: 0.8280 (t) cc_final: 0.7861 (p)
REVERT: B  485 PHE cc_start: 0.8477 (t80) cc_final: 0.8170 (t80)
REVERT: B  487 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8836 (t80)
REVERT: B  570 TRP cc_start: 0.8674 (m100) cc_final: 0.8392 (m100)
REVERT: C  272 THR cc_start: 0.8439 (m) cc_final: 0.7829 (p)
REVERT: C  413 VAL cc_start: 0.8292 (t) cc_final: 0.7861 (p)
REVERT: D  272 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.7810 (p)
REVERT: D  413 VAL cc_start: 0.8258 (t) cc_final: 0.7838 (p)
REVERT: D  645 ASN cc_start: 0.7876 (t0) cc_final: 0.7665 (t0)
  outliers start: 45
  outliers final: 37
  residues processed: 246
  average time/residue: 0.0973
  time to fit residues: 37.8091
Evaluate side-chains
  252 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 212
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  675 MET
Chi-restraints excluded: chain B residue  676 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  278 ASP
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  483 PHE
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain C residue  675 MET
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue  224 LEU
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 119 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 163 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 149 optimal weight:    8.9990
   chunk 174 optimal weight:    0.4980
   chunk 175 optimal weight:    0.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 550 HIS
B 508 ASN
B 550 HIS
C 550 HIS
D 550 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.132416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.100096 restraints weight = 24654.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.103943 restraints weight = 12145.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.106481 restraints weight = 8134.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.108065 restraints weight = 6440.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108770 restraints weight = 5595.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14892  Z= 0.140
  Angle     :  0.536   7.736  20304  Z= 0.286
  Chirality :  0.041   0.203   2368
  Planarity :  0.004   0.044   2484
  Dihedral  :  4.287  27.303   1968
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.37 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.05 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.19), residues: 1780
  helix:  1.37 (0.16), residues: 1000
  sheet: -0.34 (0.36), residues: 176
  loop : -0.78 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 464 
 TYR   0.019   0.001   TYR C 247 
 PHE   0.023   0.001   PHE D 670 
 TRP   0.009   0.001   TRP B 380 
 HIS   0.001   0.000   HIS A 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 (14876)
  covalent geometry    : angle       0.53349 /  0.29 (20260)
  SS BOND              : bond        0.00070 /  0.03 (    4)
  SS BOND              : angle       0.69009 /  0.40 (    8)
  hydrogen bonds       : bond        0.03431 /  2.28 (  829)
  hydrogen bonds       : angle       4.29143 /  3.05 ( 2403)
  link_NAG-ASN         : bond        0.00168 /  0.12 (   12)
  link_NAG-ASN         : angle       1.41269 /  1.17 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 224
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ILE cc_start: 0.9068 (mm) cc_final: 0.8866 (pt)
REVERT: A  272 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.7946 (p)
REVERT: A  274 SER cc_start: 0.8979 (m) cc_final: 0.8705 (p)
REVERT: A  413 VAL cc_start: 0.8310 (t) cc_final: 0.7821 (p)
REVERT: A  600 PHE cc_start: 0.6644 (m-80) cc_final: 0.5971 (m-80)
REVERT: B  272 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.7845 (p)
REVERT: B  413 VAL cc_start: 0.8355 (t) cc_final: 0.7884 (p)
REVERT: B  485 PHE cc_start: 0.8474 (t80) cc_final: 0.8256 (t80)
REVERT: B  570 TRP cc_start: 0.8691 (m100) cc_final: 0.8457 (m100)
REVERT: B  592 ARG cc_start: 0.7353 (tpt170) cc_final: 0.7069 (ptm-80)
REVERT: B  675 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7692 (mmp)
REVERT: C  272 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.7935 (p)
REVERT: C  413 VAL cc_start: 0.8293 (t) cc_final: 0.7786 (p)
REVERT: C  600 PHE cc_start: 0.6244 (m-80) cc_final: 0.5728 (m-80)
REVERT: D  272 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.7856 (p)
REVERT: D  413 VAL cc_start: 0.8311 (t) cc_final: 0.7827 (p)
  outliers start: 41
  outliers final: 31
  residues processed: 246
  average time/residue: 0.1012
  time to fit residues: 39.2435
Evaluate side-chains
  250 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 214
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  675 MET
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  278 ASP
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue  224 LEU
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 172 optimal weight:    3.9990
   chunk 168 optimal weight:    0.6980
   chunk 129 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0980
   chunk 169 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 108 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 550 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.100670 restraints weight = 24784.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.104374 restraints weight = 12532.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.106844 restraints weight = 8487.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108393 restraints weight = 6744.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109092 restraints weight = 5877.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.5696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14892  Z= 0.123
  Angle     :  0.523   8.206  20304  Z= 0.281
  Chirality :  0.040   0.219   2368
  Planarity :  0.004   0.043   2484
  Dihedral  :  4.197  27.938   1968
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.60 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.46 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.19), residues: 1780
  helix:  1.42 (0.16), residues: 1000
  sheet: -0.30 (0.36), residues: 176
  loop : -0.75 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 464 
 TYR   0.019   0.001   TYR C 247 
 PHE   0.023   0.001   PHE A 670 
 TRP   0.011   0.001   TRP D 366 
 HIS   0.000   0.000   HIS C 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 (14876)
  covalent geometry    : angle       0.52042 /  0.28 (20260)
  SS BOND              : bond        0.00072 /  0.04 (    4)
  SS BOND              : angle       0.58466 /  0.34 (    8)
  hydrogen bonds       : bond        0.03330 /  2.20 (  829)
  hydrogen bonds       : angle       4.22404 /  3.01 ( 2403)
  link_NAG-ASN         : bond        0.00172 /  0.12 (   12)
  link_NAG-ASN         : angle       1.31487 /  1.10 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 225
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ILE cc_start: 0.9036 (mm) cc_final: 0.8812 (mm)
REVERT: A  272 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.7942 (p)
REVERT: A  274 SER cc_start: 0.8957 (m) cc_final: 0.8711 (p)
REVERT: A  413 VAL cc_start: 0.8194 (t) cc_final: 0.7799 (p)
REVERT: A  485 PHE cc_start: 0.8374 (t80) cc_final: 0.8024 (t80)
REVERT: A  616 TYR cc_start: 0.9017 (t80) cc_final: 0.8723 (t80)
REVERT: B  235 CYS cc_start: 0.9287 (t) cc_final: 0.8889 (t)
REVERT: B  272 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.7933 (p)
REVERT: B  413 VAL cc_start: 0.8186 (t) cc_final: 0.7795 (p)
REVERT: B  570 TRP cc_start: 0.8726 (m100) cc_final: 0.8488 (m100)
REVERT: B  592 ARG cc_start: 0.7292 (tpt170) cc_final: 0.7042 (ptm-80)
REVERT: C  235 CYS cc_start: 0.9177 (t) cc_final: 0.8860 (t)
REVERT: C  272 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8143 (p)
REVERT: C  413 VAL cc_start: 0.8226 (t) cc_final: 0.7853 (p)
REVERT: C  485 PHE cc_start: 0.8352 (t80) cc_final: 0.8042 (t80)
REVERT: D  235 CYS cc_start: 0.9186 (t) cc_final: 0.8876 (t)
REVERT: D  272 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.7866 (p)
REVERT: D  413 VAL cc_start: 0.8193 (t) cc_final: 0.7813 (p)
REVERT: D  485 PHE cc_start: 0.8393 (t80) cc_final: 0.8037 (t80)
REVERT: D  600 PHE cc_start: 0.6260 (m-80) cc_final: 0.5613 (m-80)
REVERT: D  668 MET cc_start: 0.8952 (mmp) cc_final: 0.8743 (mmp)
REVERT: D  679 ILE cc_start: 0.8868 (pt) cc_final: 0.8562 (mm)
  outliers start: 39
  outliers final: 29
  residues processed: 243
  average time/residue: 0.0958
  time to fit residues: 36.7666
Evaluate side-chains
  250 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 217
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  278 ASP
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  483 PHE
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain C residue  675 MET
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue  224 LEU
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 133 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 146 optimal weight:    8.9990
   chunk 173 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 153 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 550 HIS
B 550 HIS
C 550 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.132591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.100150 restraints weight = 24850.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.104027 restraints weight = 12119.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.106542 restraints weight = 8056.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.108189 restraints weight = 6347.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.108872 restraints weight = 5505.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  14892  Z= 0.120
  Angle     :  0.531   8.614  20304  Z= 0.284
  Chirality :  0.040   0.212   2368
  Planarity :  0.004   0.042   2484
  Dihedral  :  4.195  25.963   1968
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.31 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.46 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.19), residues: 1780
  helix:  1.46 (0.16), residues: 1000
  sheet: -0.31 (0.37), residues: 176
  loop : -0.67 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 464 
 TYR   0.024   0.001   TYR D 616 
 PHE   0.023   0.001   PHE D 670 
 TRP   0.013   0.001   TRP D 366 
 HIS   0.001   0.000   HIS C 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 (14876)
  covalent geometry    : angle       0.52684 /  0.28 (20260)
  SS BOND              : bond        0.00284 /  0.14 (    4)
  SS BOND              : angle       2.47545 /  1.40 (    8)
  hydrogen bonds       : bond        0.03287 /  2.18 (  829)
  hydrogen bonds       : angle       4.19989 /  2.99 ( 2403)
  link_NAG-ASN         : bond        0.00171 /  0.12 (   12)
  link_NAG-ASN         : angle       1.29172 /  1.06 (   36)

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

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

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3560 Ramachandran restraints generated.
    1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 228
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ILE cc_start: 0.9039 (mm) cc_final: 0.8807 (mm)
REVERT: A  272 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.7935 (p)
REVERT: A  274 SER cc_start: 0.8939 (m) cc_final: 0.8711 (p)
REVERT: A  413 VAL cc_start: 0.8155 (t) cc_final: 0.7760 (p)
REVERT: A  485 PHE cc_start: 0.8370 (t80) cc_final: 0.8016 (t80)
REVERT: A  600 PHE cc_start: 0.6695 (m-80) cc_final: 0.6029 (m-80)
REVERT: A  616 TYR cc_start: 0.9027 (t80) cc_final: 0.8725 (t80)
REVERT: B  272 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.7944 (p)
REVERT: B  413 VAL cc_start: 0.8171 (t) cc_final: 0.7777 (p)
REVERT: B  592 ARG cc_start: 0.7358 (tpt170) cc_final: 0.7123 (ptm-80)
REVERT: B  600 PHE cc_start: 0.6750 (m-80) cc_final: 0.6069 (m-80)
REVERT: B  645 ASN cc_start: 0.7880 (t0) cc_final: 0.7678 (t0)
REVERT: C  272 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8213 (p)
REVERT: C  413 VAL cc_start: 0.8176 (t) cc_final: 0.7786 (p)
REVERT: C  485 PHE cc_start: 0.8327 (t80) cc_final: 0.7962 (t80)
REVERT: C  600 PHE cc_start: 0.6294 (m-80) cc_final: 0.5751 (m-80)
REVERT: D  272 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.7972 (p)
REVERT: D  413 VAL cc_start: 0.8169 (t) cc_final: 0.7770 (p)
REVERT: D  485 PHE cc_start: 0.8378 (t80) cc_final: 0.8038 (t80)
REVERT: D  600 PHE cc_start: 0.6284 (m-80) cc_final: 0.5719 (m-80)
REVERT: D  668 MET cc_start: 0.8948 (mmp) cc_final: 0.8712 (mmp)
REVERT: D  675 MET cc_start: 0.7942 (mmm) cc_final: 0.7418 (mmp)
  outliers start: 35
  outliers final: 31
  residues processed: 241
  average time/residue: 0.0968
  time to fit residues: 37.1706
Evaluate side-chains
  252 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 217
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  575 LYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  537 GLN
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  675 MET
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  278 ASP
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  537 GLN
Chi-restraints excluded: chain C residue  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain C residue  675 MET
Chi-restraints excluded: chain C residue  676 PHE
Chi-restraints excluded: chain D residue  224 LEU
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  537 GLN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 176 optimal weight:    9.9990
   chunk 11 optimal weight:    0.2980
   chunk 137 optimal weight:    0.9980
   chunk 168 optimal weight:    0.4980
   chunk 93 optimal weight:    1.9990
   chunk 156 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 152 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 550 HIS
B 550 HIS
C 550 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.133267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.101157 restraints weight = 24718.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.104896 restraints weight = 12536.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.107381 restraints weight = 8511.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108878 restraints weight = 6762.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.109905 restraints weight = 5916.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.5929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  14892  Z= 0.113
  Angle     :  0.521   8.692  20304  Z= 0.278
  Chirality :  0.040   0.185   2368
  Planarity :  0.004   0.042   2484
  Dihedral  :  4.109  25.588   1968
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.31 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.32 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.69 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.19), residues: 1780
  helix:  1.51 (0.16), residues: 1000
  sheet: -0.22 (0.37), residues: 176
  loop : -0.61 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 464 
 TYR   0.018   0.001   TYR C 247 
 PHE   0.025   0.001   PHE A 670 
 TRP   0.019   0.001   TRP B 570 
 HIS   0.001   0.000   HIS B 550 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.11 (14876)
  covalent geometry    : angle       0.51750 /  0.28 (20260)
  SS BOND              : bond        0.00065 /  0.03 (    4)
  SS BOND              : angle       1.65148 /  0.95 (    8)
  hydrogen bonds       : bond        0.03185 /  2.12 (  829)
  hydrogen bonds       : angle       4.13805 /  2.94 ( 2403)
  link_NAG-ASN         : bond        0.00179 /  0.12 (   12)
  link_NAG-ASN         : angle       1.23957 /  1.02 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2045.52 seconds
wall clock time: 36 minutes 15.76 seconds (2175.76 seconds total)