Starting phenix.real_space_refine
on Tue Nov 18 13:14:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d1w_7786/11_2025/6d1w_7786.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d1w_7786/11_2025/6d1w_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_7786/11_2025/6d1w_7786.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d1w_7786/11_2025/6d1w_7786.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6d1w_7786/11_2025/6d1w_7786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d1w_7786/11_2025/6d1w_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-2.0-5881/lib/python3.9/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 dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.33, per 1000 atoms: 0.23
  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: 1.34
  Conformation dependent library (CDL) restraints added in 680.3 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: 0.50
  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: 2.75

  Time building geometry restraints manager: 1.77 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: 8436
       16.03 -    32.07: 144
       32.07 -    48.10: 76
       48.10 -    64.13: 4
       64.13 -    80.16: 12
  Dihedral angle restraints: 8672
    sinusoidal: 3336
      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 8669 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:             0.450
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.800
  Find NCS groups from input model:        0.120
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
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  :  9.069  80.164   5204
  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
  covalent geometry    : bond        0.00746 (14876)
  covalent geometry    : angle       0.77192 (20260)
  SS BOND              : bond        0.01621 (    4)
  SS BOND              : angle       1.99287 (    8)
  hydrogen bonds       : bond        0.29263 (  829)
  hydrogen bonds       : angle       8.77863 ( 2403)
  link_NAG-ASN         : bond        0.00478 (   12)
  link_NAG-ASN         : angle       6.13889 (   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  : 0.591 
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: 0.8617 (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: 0.4923 (mmt)
REVERT: B  616 TYR cc_start: 0.8644 (t80) cc_final: 0.8399 (t80)
REVERT: B  654 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8158 (mtm-85)
REVERT: C  249 TYR cc_start: 0.8504 (t80) cc_final: 0.7840 (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: 0.8350 (m100) cc_final: 0.8143 (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: 0.1199
  time to fit residues: 76.2102
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  : 0.489 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3736 r_free = 0.3736 target = 0.135810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.103798 restraints weight = 24457.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.107842 restraints weight = 12603.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.110544 restraints weight = 8504.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.112088 restraints weight = 6642.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113333 restraints weight = 5736.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14892  Z= 0.167
  Angle     :  0.661   7.360  20304  Z= 0.361
  Chirality :  0.043   0.144   2368
  Planarity :  0.005   0.046   2484
  Dihedral  :  5.998  58.084   2228
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.58 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.92 %
    Favored  : 87.84 %
  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: -0.33 (0.18), residues: 1780
  helix:  0.28 (0.15), residues: 1000
  sheet:  0.62 (0.34), residues: 176
  loop : -1.19 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 654 
 TYR   0.021   0.002   TYR C 247 
 PHE   0.029   0.002   PHE D 472 
 TRP   0.017   0.002   TRP B 380 
 HIS   0.001   0.000   HIS B 550 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (14876)
  covalent geometry    : angle       0.64565 (20260)
  SS BOND              : bond        0.00082 (    4)
  SS BOND              : angle       1.02830 (    8)
  hydrogen bonds       : bond        0.05362 (  829)
  hydrogen bonds       : angle       5.24352 ( 2403)
  link_NAG-ASN         : bond        0.00357 (   12)
  link_NAG-ASN         : angle       3.39160 (   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
  316 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 283
  time to evaluate  : 0.494 
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  249 TYR cc_start: 0.8634 (t80) cc_final: 0.7776 (t80)
REVERT: A  555 GLN cc_start: 0.8404 (tt0) cc_final: 0.7982 (tm-30)
REVERT: A  592 ARG cc_start: 0.7284 (tpt170) cc_final: 0.6807 (ttp80)
REVERT: B  249 TYR cc_start: 0.8600 (t80) cc_final: 0.7754 (t80)
REVERT: B  487 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8336 (t80)
REVERT: B  555 GLN cc_start: 0.8365 (tt0) cc_final: 0.7950 (tm-30)
REVERT: B  592 ARG cc_start: 0.7369 (tpt170) cc_final: 0.6899 (ttp80)
REVERT: C  249 TYR cc_start: 0.8665 (t80) cc_final: 0.7885 (t80)
REVERT: C  512 VAL cc_start: 0.9462 (t) cc_final: 0.9229 (p)
REVERT: C  555 GLN cc_start: 0.8408 (tt0) cc_final: 0.7984 (tm-30)
REVERT: C  592 ARG cc_start: 0.7382 (tpt170) cc_final: 0.6904 (ttp80)
REVERT: C  598 PHE cc_start: 0.6830 (t80) cc_final: 0.6601 (m-10)
REVERT: C  603 MET cc_start: 0.7660 (ttm) cc_final: 0.7349 (ttm)
REVERT: D  249 TYR cc_start: 0.8626 (t80) cc_final: 0.7782 (t80)
REVERT: D  570 TRP cc_start: 0.8645 (m100) cc_final: 0.8157 (m100)
REVERT: D  603 MET cc_start: 0.7698 (ttm) cc_final: 0.7426 (ttm)
  outliers start: 33
  outliers final: 19
  residues processed: 304
  average time/residue: 0.1240
  time to fit residues: 55.8311
Evaluate side-chains
  237 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 217
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 132 optimal weight:    0.5980
   chunk 176 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 154 optimal weight:    7.9990
   chunk 130 optimal weight:    0.7980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 434 ASN
A 550 HIS
A 578 ASN
B 434 ASN
B 550 HIS
B 578 ASN
C 434 ASN
C 542 GLN
C 550 HIS
C 578 ASN
D 434 ASN
D 550 HIS
D 578 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.133487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.101366 restraints weight = 24855.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.105377 restraints weight = 12371.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108006 restraints weight = 8246.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.109759 restraints weight = 6457.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110569 restraints weight = 5560.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  14892  Z= 0.138
  Angle     :  0.584   7.316  20304  Z= 0.314
  Chirality :  0.042   0.131   2368
  Planarity :  0.004   0.052   2484
  Dihedral  :  4.478  29.199   2220
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.92 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.62 %
    Favored  : 86.07 %
  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:  0.41 (0.19), residues: 1780
  helix:  1.06 (0.16), residues: 988
  sheet:  0.23 (0.33), residues: 176
  loop : -0.95 (0.24), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 464 
 TYR   0.020   0.002   TYR C 247 
 PHE   0.014   0.001   PHE A 472 
 TRP   0.011   0.001   TRP B 380 
 HIS   0.001   0.001   HIS C 550 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (14876)
  covalent geometry    : angle       0.57486 (20260)
  SS BOND              : bond        0.00115 (    4)
  SS BOND              : angle       0.92568 (    8)
  hydrogen bonds       : bond        0.04209 (  829)
  hydrogen bonds       : angle       4.67110 ( 2403)
  link_NAG-ASN         : bond        0.00266 (   12)
  link_NAG-ASN         : angle       2.51521 (   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
  284 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 250
  time to evaluate  : 0.580 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8572 (t80) cc_final: 0.7591 (t80)
REVERT: A  272 THR cc_start: 0.8334 (m) cc_final: 0.7718 (p)
REVERT: A  518 SER cc_start: 0.9368 (m) cc_final: 0.9055 (p)
REVERT: A  555 GLN cc_start: 0.8300 (tt0) cc_final: 0.8025 (tm-30)
REVERT: A  583 MET cc_start: 0.6319 (tmm) cc_final: 0.5927 (ttt)
REVERT: A  631 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7594 (tp30)
REVERT: B  249 TYR cc_start: 0.8567 (t80) cc_final: 0.7753 (t80)
REVERT: B  272 THR cc_start: 0.8299 (m) cc_final: 0.7636 (p)
REVERT: B  487 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8562 (t80)
REVERT: B  518 SER cc_start: 0.9372 (m) cc_final: 0.9076 (p)
REVERT: B  570 TRP cc_start: 0.8661 (m100) cc_final: 0.8394 (m100)
REVERT: B  583 MET cc_start: 0.6274 (tmm) cc_final: 0.5666 (ttt)
REVERT: B  592 ARG cc_start: 0.7333 (tpt170) cc_final: 0.6838 (ttp80)
REVERT: C  249 TYR cc_start: 0.8589 (t80) cc_final: 0.7736 (t80)
REVERT: C  272 THR cc_start: 0.8359 (m) cc_final: 0.7723 (p)
REVERT: C  518 SER cc_start: 0.9361 (m) cc_final: 0.9033 (p)
REVERT: C  555 GLN cc_start: 0.8383 (tt0) cc_final: 0.8075 (tm-30)
REVERT: C  592 ARG cc_start: 0.7405 (tpt170) cc_final: 0.6898 (ttp80)
REVERT: C  631 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7574 (tp30)
REVERT: D  249 TYR cc_start: 0.8582 (t80) cc_final: 0.7664 (t80)
REVERT: D  272 THR cc_start: 0.8336 (m) cc_final: 0.7714 (p)
REVERT: D  518 SER cc_start: 0.9364 (m) cc_final: 0.9050 (p)
REVERT: D  555 GLN cc_start: 0.8300 (tt0) cc_final: 0.8035 (tm-30)
REVERT: D  631 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7586 (tp30)
  outliers start: 34
  outliers final: 19
  residues processed: 279
  average time/residue: 0.1109
  time to fit residues: 48.0594
Evaluate side-chains
  235 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 212
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
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  631 GLU
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  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  597 LEU
Chi-restraints excluded: chain C residue  631 GLU
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  434 ASN
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  631 GLU
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:    5.9990
   chunk 165 optimal weight:    2.9990
   chunk 131 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9990
   chunk 90 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 133 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 434 ASN
A 537 GLN
B 434 ASN
C 434 ASN
C 537 GLN
C 542 GLN
D 434 ASN
D 537 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.131142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.098756 restraints weight = 25027.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.102661 restraints weight = 12406.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.105276 restraints weight = 8259.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.106847 restraints weight = 6483.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.107887 restraints weight = 5628.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  14892  Z= 0.151
  Angle     :  0.571   7.291  20304  Z= 0.305
  Chirality :  0.040   0.130   2368
  Planarity :  0.004   0.048   2484
  Dihedral  :  4.341  26.929   2220
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.64 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.13 %
    Favored  : 83.42 %
  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:  0.52 (0.19), residues: 1780
  helix:  1.20 (0.16), residues: 992
  sheet:  0.01 (0.34), residues: 176
  loop : -0.91 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 464 
 TYR   0.019   0.001   TYR C 247 
 PHE   0.015   0.001   PHE B 670 
 TRP   0.010   0.001   TRP C 507 
 HIS   0.001   0.000   HIS C 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (14876)
  covalent geometry    : angle       0.56503 (20260)
  SS BOND              : bond        0.00045 (    4)
  SS BOND              : angle       0.81114 (    8)
  hydrogen bonds       : bond        0.03884 (  829)
  hydrogen bonds       : angle       4.51717 ( 2403)
  link_NAG-ASN         : bond        0.00212 (   12)
  link_NAG-ASN         : angle       2.07447 (   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
  275 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 239
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 SER cc_start: 0.9388 (m) cc_final: 0.9108 (p)
REVERT: B  249 TYR cc_start: 0.8619 (t80) cc_final: 0.7614 (t80)
REVERT: B  487 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8728 (t80)
REVERT: B  592 ARG cc_start: 0.7342 (tpt170) cc_final: 0.6778 (ttp80)
REVERT: B  600 PHE cc_start: 0.6439 (m-80) cc_final: 0.5897 (m-80)
REVERT: C  249 TYR cc_start: 0.8613 (t80) cc_final: 0.7497 (t80)
REVERT: C  518 SER cc_start: 0.9389 (m) cc_final: 0.9095 (p)
REVERT: C  583 MET cc_start: 0.6356 (tmm) cc_final: 0.5481 (ttt)
REVERT: C  592 ARG cc_start: 0.7270 (tpt170) cc_final: 0.6777 (ttp80)
REVERT: D  249 TYR cc_start: 0.8602 (t80) cc_final: 0.7478 (t80)
REVERT: D  518 SER cc_start: 0.9393 (m) cc_final: 0.9109 (p)
REVERT: D  583 MET cc_start: 0.6452 (tmm) cc_final: 0.5585 (ttt)
  outliers start: 36
  outliers final: 29
  residues processed: 261
  average time/residue: 0.1086
  time to fit residues: 44.0749
Evaluate side-chains
  247 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 217
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ASP
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  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  434 ASN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  487 TYR
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  252 MET
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  597 LEU
Chi-restraints excluded: chain C residue  640 ILE
Chi-restraints excluded: chain D residue  252 MET
Chi-restraints excluded: chain D residue  278 ASP
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  597 LEU
Chi-restraints excluded: chain D residue  607 ILE
Chi-restraints excluded: chain D residue  640 ILE
Chi-restraints excluded: chain D residue  673 LEU
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 128 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 109 optimal weight:    5.9990
   chunk 157 optimal weight:    0.6980
   overall best weight:    3.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
A 550 HIS
B 508 ASN
B 550 HIS
C 508 ASN
C 550 HIS
D 508 ASN
D 550 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.125352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.093018 restraints weight = 25262.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.096566 restraints weight = 12612.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.098939 restraints weight = 8565.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.100314 restraints weight = 6814.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.101059 restraints weight = 5988.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.5279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046  14892  Z= 0.301
  Angle     :  0.677   9.135  20304  Z= 0.359
  Chirality :  0.044   0.138   2368
  Planarity :  0.005   0.052   2484
  Dihedral  :  4.974  29.476   2220
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.09 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.33 %
    Favored  : 82.00 %
  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:  0.18 (0.19), residues: 1780
  helix:  0.89 (0.15), residues: 992
  sheet: -0.35 (0.33), residues: 176
  loop : -0.91 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 420 
 TYR   0.023   0.002   TYR C 249 
 PHE   0.025   0.002   PHE C 670 
 TRP   0.020   0.002   TRP B 380 
 HIS   0.002   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00682 (14876)
  covalent geometry    : angle       0.67256 (20260)
  SS BOND              : bond        0.00062 (    4)
  SS BOND              : angle       1.09783 (    8)
  hydrogen bonds       : bond        0.04409 (  829)
  hydrogen bonds       : angle       4.74890 ( 2403)
  link_NAG-ASN         : bond        0.00161 (   12)
  link_NAG-ASN         : angle       1.91046 (   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
  269 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 215
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 THR cc_start: 0.8742 (m) cc_final: 0.8250 (p)
REVERT: A  487 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8870 (t80)
REVERT: A  518 SER cc_start: 0.9426 (m) cc_final: 0.9182 (p)
REVERT: A  583 MET cc_start: 0.6638 (tmm) cc_final: 0.6034 (ttt)
REVERT: A  600 PHE cc_start: 0.6246 (m-80) cc_final: 0.5767 (m-80)
REVERT: A  679 ILE cc_start: 0.8970 (mm) cc_final: 0.8716 (mm)
REVERT: B  272 THR cc_start: 0.8682 (m) cc_final: 0.8155 (p)
REVERT: B  487 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.8811 (t80)
REVERT: B  583 MET cc_start: 0.6626 (tmm) cc_final: 0.6028 (ttt)
REVERT: B  592 ARG cc_start: 0.7354 (tpt170) cc_final: 0.6988 (ttp80)
REVERT: B  600 PHE cc_start: 0.6715 (m-80) cc_final: 0.6022 (m-80)
REVERT: B  605 PHE cc_start: 0.8077 (m-10) cc_final: 0.7837 (m-80)
REVERT: B  645 ASN cc_start: 0.7887 (t0) cc_final: 0.7664 (t0)
REVERT: C  255 GLN cc_start: 0.8333 (mt0) cc_final: 0.8100 (mt0)
REVERT: C  272 THR cc_start: 0.8760 (m) cc_final: 0.8261 (p)
REVERT: C  487 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8873 (t80)
REVERT: C  518 SER cc_start: 0.9432 (m) cc_final: 0.9185 (p)
REVERT: C  592 ARG cc_start: 0.7376 (tpt170) cc_final: 0.6979 (ttp80)
REVERT: D  255 GLN cc_start: 0.8326 (mt0) cc_final: 0.8095 (mt0)
REVERT: D  272 THR cc_start: 0.8744 (m) cc_final: 0.8256 (p)
REVERT: D  487 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8824 (t80)
REVERT: D  583 MET cc_start: 0.6591 (tmm) cc_final: 0.5968 (ttt)
REVERT: D  600 PHE cc_start: 0.6362 (m-80) cc_final: 0.5727 (m-80)
REVERT: D  675 MET cc_start: 0.7946 (mmm) cc_final: 0.7306 (mmp)
  outliers start: 54
  outliers final: 39
  residues processed: 249
  average time/residue: 0.1115
  time to fit residues: 43.0778
Evaluate side-chains
  247 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 204
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  487 TYR
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  233 VAL
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  575 LYS
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  659 ILE
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  487 TYR
Chi-restraints excluded: chain C residue  547 ASN
Chi-restraints excluded: chain C residue  575 LYS
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  252 MET
Chi-restraints excluded: chain D residue  278 ASP
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  487 TYR
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  547 ASN
Chi-restraints excluded: chain D residue  575 LYS
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  607 ILE
Chi-restraints excluded: chain D residue  640 ILE
Chi-restraints excluded: chain D residue  659 ILE
Chi-restraints excluded: chain D residue  673 LEU
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 126 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 173 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 80 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 136 optimal weight:   10.0000
   chunk 115 optimal weight:    7.9990
   chunk 168 optimal weight:    0.9990
   overall best weight:    1.2586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.097226 restraints weight = 24810.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.101073 restraints weight = 12030.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.103537 restraints weight = 7989.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.105103 restraints weight = 6316.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.105914 restraints weight = 5485.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.5457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14892  Z= 0.146
  Angle     :  0.565   7.717  20304  Z= 0.301
  Chirality :  0.040   0.185   2368
  Planarity :  0.004   0.049   2484
  Dihedral  :  4.398  25.003   2220
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.09 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.51 %
    Favored  : 80.64 %
  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:  0.51 (0.19), residues: 1780
  helix:  1.17 (0.16), residues: 988
  sheet: -0.46 (0.35), residues: 176
  loop : -0.69 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.018   0.001   TYR C 247 
 PHE   0.020   0.001   PHE D 576 
 TRP   0.011   0.001   TRP D 366 
 HIS   0.001   0.000   HIS C 550 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (14876)
  covalent geometry    : angle       0.56119 (20260)
  SS BOND              : bond        0.00741 (    4)
  SS BOND              : angle       1.66712 (    8)
  hydrogen bonds       : bond        0.03727 (  829)
  hydrogen bonds       : angle       4.48587 ( 2403)
  link_NAG-ASN         : bond        0.00159 (   12)
  link_NAG-ASN         : angle       1.56530 (   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
  266 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 224
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 GLN cc_start: 0.8324 (mt0) cc_final: 0.8015 (mt0)
REVERT: A  272 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8263 (p)
REVERT: A  487 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8818 (t80)
REVERT: A  583 MET cc_start: 0.6705 (tmm) cc_final: 0.6116 (ttt)
REVERT: A  600 PHE cc_start: 0.6293 (m-80) cc_final: 0.5829 (m-80)
REVERT: B  272 THR cc_start: 0.8750 (m) cc_final: 0.8253 (p)
REVERT: B  487 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8780 (t80)
REVERT: B  583 MET cc_start: 0.6700 (tmm) cc_final: 0.6036 (ttt)
REVERT: B  645 ASN cc_start: 0.7833 (t0) cc_final: 0.7569 (t0)
REVERT: C  255 GLN cc_start: 0.8276 (mt0) cc_final: 0.7982 (mt0)
REVERT: C  272 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8349 (p)
REVERT: C  487 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8822 (t80)
REVERT: C  583 MET cc_start: 0.6525 (tmm) cc_final: 0.5847 (ttt)
REVERT: C  600 PHE cc_start: 0.6227 (m-80) cc_final: 0.5700 (m-80)
REVERT: D  255 GLN cc_start: 0.8276 (mt0) cc_final: 0.8051 (mt0)
REVERT: D  272 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8255 (p)
REVERT: D  487 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8812 (t80)
REVERT: D  583 MET cc_start: 0.6675 (tmm) cc_final: 0.6299 (ttt)
  outliers start: 42
  outliers final: 31
  residues processed: 246
  average time/residue: 0.1198
  time to fit residues: 44.8919
Evaluate side-chains
  243 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
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  278 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  224 LEU
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  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  252 MET
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  487 TYR
Chi-restraints excluded: chain C residue  514 ILE
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  252 MET
Chi-restraints excluded: chain D residue  272 THR
Chi-restraints excluded: chain D residue  278 ASP
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  484 ILE
Chi-restraints excluded: chain D residue  487 TYR
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 150 optimal weight:    6.9990
   chunk 117 optimal weight:    0.0970
   chunk 178 optimal weight:    0.8980
   chunk 133 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 73 optimal weight:    0.7980
   chunk 153 optimal weight:    0.9980
   chunk 127 optimal weight:    0.8980
   overall best weight:    0.7378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.100219 restraints weight = 24493.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.104014 restraints weight = 12458.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.106529 restraints weight = 8460.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.108045 restraints weight = 6732.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.109026 restraints weight = 5874.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.5666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  14892  Z= 0.119
  Angle     :  0.541   8.672  20304  Z= 0.289
  Chirality :  0.040   0.214   2368
  Planarity :  0.004   0.048   2484
  Dihedral  :  4.174  24.786   2220
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.10 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.46 %
    Favored  : 79.69 %
  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:  0.50 (0.19), residues: 1780
  helix:  1.22 (0.16), residues: 1004
  sheet: -0.50 (0.35), residues: 176
  loop : -0.86 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.018   0.001   TYR C 247 
 PHE   0.018   0.001   PHE B 576 
 TRP   0.009   0.001   TRP C 366 
 HIS   0.000   0.000   HIS B 550 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (14876)
  covalent geometry    : angle       0.53775 (20260)
  SS BOND              : bond        0.00224 (    4)
  SS BOND              : angle       1.45672 (    8)
  hydrogen bonds       : bond        0.03442 (  829)
  hydrogen bonds       : angle       4.33214 ( 2403)
  link_NAG-ASN         : bond        0.00194 (   12)
  link_NAG-ASN         : angle       1.42332 (   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
  263 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 221
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 GLN cc_start: 0.8330 (mt0) cc_final: 0.7989 (mt0)
REVERT: A  272 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8231 (p)
REVERT: A  600 PHE cc_start: 0.6130 (m-80) cc_final: 0.5743 (m-80)
REVERT: A  616 TYR cc_start: 0.9035 (t80) cc_final: 0.8807 (t80)
REVERT: B  272 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8215 (p)
REVERT: B  487 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8774 (t80)
REVERT: B  590 MET cc_start: 0.5924 (mtt) cc_final: 0.5617 (mtt)
REVERT: B  592 ARG cc_start: 0.7393 (tpt170) cc_final: 0.7132 (ptm-80)
REVERT: C  255 GLN cc_start: 0.8267 (mt0) cc_final: 0.7974 (mt0)
REVERT: C  272 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8335 (p)
REVERT: C  583 MET cc_start: 0.6607 (tmm) cc_final: 0.5922 (ttt)
REVERT: C  645 ASN cc_start: 0.7869 (t0) cc_final: 0.7665 (t0)
REVERT: D  255 GLN cc_start: 0.8357 (mt0) cc_final: 0.8069 (mt0)
REVERT: D  272 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8245 (p)
REVERT: D  485 PHE cc_start: 0.8519 (t80) cc_final: 0.8194 (t80)
REVERT: D  583 MET cc_start: 0.6621 (tmm) cc_final: 0.6152 (ttt)
REVERT: D  616 TYR cc_start: 0.9028 (t80) cc_final: 0.8800 (t80)
  outliers start: 42
  outliers final: 32
  residues processed: 240
  average time/residue: 0.1134
  time to fit residues: 42.2454
Evaluate side-chains
  245 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 208
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
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  278 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  224 LEU
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  484 ILE
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  511 ASP
Chi-restraints excluded: chain B residue  514 ILE
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  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  597 LEU
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  278 ASP
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  511 ASP
Chi-restraints excluded: chain D residue  514 ILE
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:    5.9990
   chunk 119 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 163 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 149 optimal weight:    7.9990
   chunk 174 optimal weight:    4.9990
   chunk 175 optimal weight:    0.6980
   overall best weight:    2.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 550 HIS
B 550 HIS
C 550 HIS
D 550 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.127597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.095242 restraints weight = 24864.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.098937 restraints weight = 12347.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.101369 restraints weight = 8287.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.102594 restraints weight = 6562.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103698 restraints weight = 5779.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.5738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  14892  Z= 0.219
  Angle     :  0.601   7.486  20304  Z= 0.317
  Chirality :  0.042   0.231   2368
  Planarity :  0.004   0.050   2484
  Dihedral  :  4.468  26.851   2220
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.20 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.00 %
    Favored  : 79.08 %
  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:  0.52 (0.19), residues: 1780
  helix:  1.10 (0.15), residues: 1016
  sheet: -0.59 (0.35), residues: 176
  loop : -0.55 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 399 
 TYR   0.019   0.002   TYR C 247 
 PHE   0.024   0.002   PHE A 670 
 TRP   0.014   0.002   TRP B 570 
 HIS   0.002   0.001   HIS B 550 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (14876)
  covalent geometry    : angle       0.59638 (20260)
  SS BOND              : bond        0.00320 (    4)
  SS BOND              : angle       2.28408 (    8)
  hydrogen bonds       : bond        0.03845 (  829)
  hydrogen bonds       : angle       4.43709 ( 2403)
  link_NAG-ASN         : bond        0.00117 (   12)
  link_NAG-ASN         : angle       1.47777 (   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
  253 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 210
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 GLN cc_start: 0.8373 (mt0) cc_final: 0.8066 (mt0)
REVERT: A  272 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8243 (p)
REVERT: A  600 PHE cc_start: 0.6174 (m-80) cc_final: 0.5838 (m-80)
REVERT: B  272 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8351 (p)
REVERT: B  487 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8722 (t80)
REVERT: B  592 ARG cc_start: 0.7495 (tpt170) cc_final: 0.7022 (ttp80)
REVERT: C  255 GLN cc_start: 0.8317 (mt0) cc_final: 0.8061 (mt0)
REVERT: C  272 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8255 (p)
REVERT: C  583 MET cc_start: 0.6509 (tmm) cc_final: 0.5861 (ttt)
REVERT: C  645 ASN cc_start: 0.7932 (t0) cc_final: 0.7709 (t0)
REVERT: D  255 GLN cc_start: 0.8347 (mt0) cc_final: 0.8071 (mt0)
REVERT: D  272 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8249 (p)
REVERT: D  485 PHE cc_start: 0.8512 (t80) cc_final: 0.8208 (t80)
REVERT: D  583 MET cc_start: 0.6506 (tmm) cc_final: 0.5856 (ttt)
  outliers start: 43
  outliers final: 35
  residues processed: 229
  average time/residue: 0.1107
  time to fit residues: 39.4099
Evaluate side-chains
  241 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 201
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  224 LEU
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  473 LEU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  514 ILE
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  640 ILE
Chi-restraints excluded: chain B residue  659 ILE
Chi-restraints excluded: chain B residue  673 LEU
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  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  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  278 ASP
Chi-restraints excluded: chain D residue  382 ILE
Chi-restraints excluded: chain D residue  419 THR
Chi-restraints excluded: chain D residue  597 LEU
Chi-restraints excluded: chain D residue  640 ILE
Chi-restraints excluded: chain D residue  673 LEU
Chi-restraints excluded: chain D residue  676 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 172 optimal weight:    0.8980
   chunk 168 optimal weight:    0.9990
   chunk 129 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 169 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.099361 restraints weight = 24993.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103065 restraints weight = 12811.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105523 restraints weight = 8729.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.106995 restraints weight = 6959.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.107708 restraints weight = 6091.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.5908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14892  Z= 0.121
  Angle     :  0.531   7.637  20304  Z= 0.282
  Chirality :  0.040   0.215   2368
  Planarity :  0.004   0.047   2484
  Dihedral  :  4.146  24.843   2220
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.88 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.73 %
    Favored  : 79.69 %
  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:  0.56 (0.19), residues: 1780
  helix:  1.18 (0.16), residues: 1020
  sheet: -0.57 (0.36), residues: 176
  loop : -0.66 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 464 
 TYR   0.018   0.001   TYR C 247 
 PHE   0.018   0.001   PHE B 576 
 TRP   0.016   0.001   TRP A 570 
 HIS   0.001   0.001   HIS C 550 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (14876)
  covalent geometry    : angle       0.52774 (20260)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       1.07725 (    8)
  hydrogen bonds       : bond        0.03388 (  829)
  hydrogen bonds       : angle       4.27457 ( 2403)
  link_NAG-ASN         : bond        0.00156 (   12)
  link_NAG-ASN         : angle       1.32761 (   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
  256 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 218
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 GLN cc_start: 0.8321 (mt0) cc_final: 0.7993 (mt0)
REVERT: A  272 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8248 (p)
REVERT: A  413 VAL cc_start: 0.8458 (t) cc_final: 0.8163 (p)
REVERT: A  600 PHE cc_start: 0.6277 (m-80) cc_final: 0.6031 (m-80)
REVERT: B  255 GLN cc_start: 0.8234 (mt0) cc_final: 0.7939 (mt0)
REVERT: B  272 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8338 (p)
REVERT: B  413 VAL cc_start: 0.8527 (t) cc_final: 0.8222 (p)
REVERT: B  485 PHE cc_start: 0.8518 (t80) cc_final: 0.8173 (t80)
REVERT: B  487 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8762 (t80)
REVERT: B  592 ARG cc_start: 0.7365 (tpt170) cc_final: 0.7108 (ptm-80)
REVERT: C  255 GLN cc_start: 0.8249 (mt0) cc_final: 0.7958 (mt0)
REVERT: C  272 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8303 (p)
REVERT: C  413 VAL cc_start: 0.8469 (t) cc_final: 0.8174 (p)
REVERT: C  583 MET cc_start: 0.6496 (tmm) cc_final: 0.5897 (ttt)
REVERT: D  255 GLN cc_start: 0.8358 (mt0) cc_final: 0.8085 (mt0)
REVERT: D  272 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8294 (p)
REVERT: D  413 VAL cc_start: 0.8459 (t) cc_final: 0.8162 (p)
REVERT: D  583 MET cc_start: 0.6594 (tmm) cc_final: 0.6077 (ttt)
REVERT: D  600 PHE cc_start: 0.6794 (m-80) cc_final: 0.6100 (m-80)
REVERT: D  645 ASN cc_start: 0.7892 (t0) cc_final: 0.7643 (t0)
  outliers start: 38
  outliers final: 26
  residues processed: 239
  average time/residue: 0.1099
  time to fit residues: 40.9658
Evaluate side-chains
  234 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  252 MET
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  514 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  224 LEU
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  484 ILE
Chi-restraints excluded: chain B residue  487 TYR
Chi-restraints excluded: chain B residue  514 ILE
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  252 MET
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  597 LEU
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  511 ASP
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  597 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 131 optimal weight:    0.0470
   chunk 48 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 133 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 146 optimal weight:    4.9990
   chunk 173 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
B 323 GLN
B 550 HIS
C 323 GLN
D 323 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.132755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.100848 restraints weight = 24814.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.104617 restraints weight = 12588.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107116 restraints weight = 8526.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.108476 restraints weight = 6761.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109587 restraints weight = 5953.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.6001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  14892  Z= 0.113
  Angle     :  0.528   8.815  20304  Z= 0.280
  Chirality :  0.040   0.188   2368
  Planarity :  0.004   0.046   2484
  Dihedral  :  3.985  24.860   2220
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.48 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.21 %
    Favored  : 79.55 %
  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:  1.22 (0.16), residues: 1032
  sheet: -0.51 (0.37), residues: 176
  loop : -0.65 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.018   0.001   TYR C 247 
 PHE   0.024   0.001   PHE A 670 
 TRP   0.017   0.001   TRP A 570 
 HIS   0.001   0.000   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (14876)
  covalent geometry    : angle       0.52505 (20260)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       1.05425 (    8)
  hydrogen bonds       : bond        0.03279 (  829)
  hydrogen bonds       : angle       4.20197 ( 2403)
  link_NAG-ASN         : bond        0.00162 (   12)
  link_NAG-ASN         : angle       1.27335 (   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
  260 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 227
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8200 (p)
REVERT: A  413 VAL cc_start: 0.8389 (t) cc_final: 0.8019 (p)
REVERT: A  603 MET cc_start: 0.6415 (ttp) cc_final: 0.6152 (tmm)
REVERT: A  645 ASN cc_start: 0.7931 (t0) cc_final: 0.7581 (t0)
REVERT: A  675 MET cc_start: 0.7637 (mmp) cc_final: 0.6965 (ttp)
REVERT: B  235 CYS cc_start: 0.9055 (t) cc_final: 0.8733 (t)
REVERT: B  272 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8338 (p)
REVERT: B  413 VAL cc_start: 0.8368 (t) cc_final: 0.8011 (p)
REVERT: B  485 PHE cc_start: 0.8496 (t80) cc_final: 0.8155 (t80)
REVERT: B  592 ARG cc_start: 0.7393 (tpt170) cc_final: 0.7179 (ptm-80)
REVERT: C  255 GLN cc_start: 0.8358 (mt0) cc_final: 0.8084 (mt0)
REVERT: C  272 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8265 (p)
REVERT: C  278 ASP cc_start: 0.8622 (m-30) cc_final: 0.7783 (m-30)
REVERT: C  413 VAL cc_start: 0.8397 (t) cc_final: 0.8031 (p)
REVERT: C  583 MET cc_start: 0.6431 (tmm) cc_final: 0.5819 (ttt)
REVERT: C  600 PHE cc_start: 0.6295 (m-80) cc_final: 0.5720 (m-80)
REVERT: D  255 GLN cc_start: 0.8434 (mt0) cc_final: 0.8140 (mt0)
REVERT: D  272 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8218 (p)
REVERT: D  413 VAL cc_start: 0.8385 (t) cc_final: 0.8013 (p)
REVERT: D  583 MET cc_start: 0.6446 (tmm) cc_final: 0.5954 (ttt)
  outliers start: 33
  outliers final: 23
  residues processed: 242
  average time/residue: 0.1102
  time to fit residues: 41.7637
Evaluate side-chains
  244 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 217
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
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  514 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  382 ILE
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  514 ILE
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  272 THR
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  484 ILE
Chi-restraints excluded: chain C residue  514 ILE
Chi-restraints excluded: chain C residue  575 LYS
Chi-restraints excluded: chain C residue  597 LEU
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  511 ASP
Chi-restraints excluded: chain D residue  514 ILE
Chi-restraints excluded: chain D residue  597 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 109 optimal weight:    0.2980
   chunk 176 optimal weight:    0.0570
   chunk 11 optimal weight:    0.0070
   chunk 137 optimal weight:    8.9990
   chunk 168 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 156 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 114 optimal weight:   10.0000
   chunk 152 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
B 550 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.134223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.102435 restraints weight = 24661.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.106227 restraints weight = 12609.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.108769 restraints weight = 8542.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.110272 restraints weight = 6766.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.111322 restraints weight = 5901.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.6121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  14892  Z= 0.108
  Angle     :  0.530   8.565  20304  Z= 0.280
  Chirality :  0.040   0.193   2368
  Planarity :  0.004   0.045   2484
  Dihedral  :  3.904  24.275   2220
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.37 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.23 %
    Favored  : 78.80 %
  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:  0.70 (0.20), residues: 1780
  helix:  1.30 (0.16), residues: 1028
  sheet: -0.46 (0.37), residues: 176
  loop : -0.66 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.018   0.001   TYR C 247 
 PHE   0.021   0.001   PHE C 485 
 TRP   0.014   0.001   TRP A 570 
 HIS   0.001   0.000   HIS C 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (14876)
  covalent geometry    : angle       0.52802 (20260)
  SS BOND              : bond        0.00118 (    4)
  SS BOND              : angle       0.84391 (    8)
  hydrogen bonds       : bond        0.03191 (  829)
  hydrogen bonds       : angle       4.17525 ( 2403)
  link_NAG-ASN         : bond        0.00196 (   12)
  link_NAG-ASN         : angle       1.19652 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2255.95 seconds
wall clock time: 39 minutes 58.23 seconds (2398.23 seconds total)