Starting phenix.real_space_refine
on Wed Mar  4 11:26:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ngb_12311/03_2026/7ngb_12311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ngb_12311/03_2026/7ngb_12311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ngb_12311/03_2026/7ngb_12311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ngb_12311/03_2026/7ngb_12311.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ngb_12311/03_2026/7ngb_12311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ngb_12311/03_2026/7ngb_12311.map"
  }
  resolution = 3.64
  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=  -0.002 sd=   0.042
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      86      5.16       5
     C    8568      2.51       5
     N    2178      2.21       5
     O    2312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13144
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 859, 6519
          Classifications: {'peptide': 859}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 33, 'TRANS': 825}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 128
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 59
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 5.95, per 1000 atoms: 0.45
  Number of scatterers: 13144
  At special positions: 0
  Unit cell: (112.035, 103.499, 150.447, 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      86     16.00
     O    2312      8.00
     N    2178      7.00
     C    8568      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 640 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 339 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 359 " - pdb=" SG  CYS A 369 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 640 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 324 " - pdb=" SG  CYS B 339 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 359 " - pdb=" SG  CYS B 369 " distance=2.03

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A1101 " - " ASN A 377 "
      " NAG B1101 " - " ASN B 377 "
      " NAG C   1 " - " ASN A 328 "
      " NAG D   1 " - " ASN B 328 "
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 550.0 milliseconds
  

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3156

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 8 sheets defined
      61.6% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 135 through 149
      removed outlier: 5.284A  pdb=" N   LEU A 142 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
      Proline residue:  A 143  - end of helix
    Processing helix  chain 'A' and resid 151 through 156
    Processing helix  chain 'A' and resid 156 through 193
      removed outlier: 6.478A  pdb=" N   VAL A 166 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   LEU A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   GLN A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 243
      removed outlier: 3.571A  pdb=" N   MET A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 211  - end of helix
    Processing helix  chain 'A' and resid 260 through 284
    Processing helix  chain 'A' and resid 285 through 314
      removed outlier: 3.803A  pdb=" N   VAL A 289 " --> pdb=" O   GLY A 285 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   SER A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   LEU A 295 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 359
    Processing helix  chain 'A' and resid 370 through 376
    Processing helix  chain 'A' and resid 386 through 394
      removed outlier: 4.204A  pdb=" N   GLY A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   ILE A 391 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE A 392 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 393 " --> pdb=" O   GLY A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 442
      removed outlier: 3.691A  pdb=" N   GLY A 439 " --> pdb=" O   THR A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 445
      No H-bonds generated for 'chain 'A' and resid 443 through 445'
    Processing helix  chain 'A' and resid 447 through 453
    Processing helix  chain 'A' and resid 460 through 491
      Proline residue:  A 466  - end of helix
      removed outlier: 3.736A  pdb=" N   VAL A 485 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 513
    Processing helix  chain 'A' and resid 517 through 550
      removed outlier: 4.396A  pdb=" N   ILE A 521 " --> pdb=" O   SER A 517 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE A 526 " --> pdb=" O   VAL A 522 " (cutoff:3.500A)
      Proline residue:  A 541  - end of helix
    Processing helix  chain 'A' and resid 554 through 561
      removed outlier: 3.945A  pdb=" N   VAL A 558 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   HIS A 561 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 584
      removed outlier: 3.547A  pdb=" N   LEU A 572 " --> pdb=" O   PRO A 568 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU A 573 " --> pdb=" O   THR A 569 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU A 574 " --> pdb=" O   TRP A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 616
      Proline residue:  A 593  - end of helix
      removed outlier: 3.828A  pdb=" N   CYS A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 648
      removed outlier: 3.572A  pdb=" N   SER A 633 " --> pdb=" O   HIS A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 675
      removed outlier: 3.630A  pdb=" N   ILE A 653 " --> pdb=" O   TRP A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 696
      removed outlier: 3.585A  pdb=" N   GLU A 696 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 734
      removed outlier: 4.293A  pdb=" N   LEU A 726 " --> pdb=" O   HIS A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 770
    Processing helix  chain 'A' and resid 783 through 795
      removed outlier: 4.034A  pdb=" N   GLN A 793 " --> pdb=" O   SER A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 835
      removed outlier: 3.597A  pdb=" N   PHE A 825 " --> pdb=" O   ALA A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 844 through 848
    Processing helix  chain 'A' and resid 868 through 881
      removed outlier: 4.055A  pdb=" N   LEU A 872 " --> pdb=" O   ASP A 868 " (cutoff:3.500A)
      Proline residue:  A 876  - end of helix
    Processing helix  chain 'A' and resid 901 through 917
      removed outlier: 3.508A  pdb=" N   ARG A 917 " --> pdb=" O   LEU A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1048
      removed outlier: 3.939A  pdb=" N   LYS A1038 " --> pdb=" O   HIS A1034 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1065
      No H-bonds generated for 'chain 'A' and resid 1063 through 1065'
    Processing helix  chain 'A' and resid 1066 through 1078
    Processing helix  chain 'B' and resid 135 through 149
      removed outlier: 5.283A  pdb=" N   LEU B 142 " --> pdb=" O   MET B 138 " (cutoff:3.500A)
      Proline residue:  B 143  - end of helix
    Processing helix  chain 'B' and resid 151 through 156
    Processing helix  chain 'B' and resid 156 through 193
      removed outlier: 6.480A  pdb=" N   VAL B 166 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
      removed outlier: 9.393A  pdb=" N   LEU B 167 " --> pdb=" O   THR B 163 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLN B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 243
      removed outlier: 3.571A  pdb=" N   MET B 204 " --> pdb=" O   GLY B 200 " (cutoff:3.500A)
      Proline residue:  B 211  - end of helix
    Processing helix  chain 'B' and resid 260 through 284
    Processing helix  chain 'B' and resid 285 through 314
      removed outlier: 3.802A  pdb=" N   VAL B 289 " --> pdb=" O   GLY B 285 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   SER B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   LEU B 295 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 359
    Processing helix  chain 'B' and resid 370 through 376
    Processing helix  chain 'B' and resid 386 through 394
      removed outlier: 4.204A  pdb=" N   GLY B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   ILE B 391 " --> pdb=" O   ALA B 388 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE B 392 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR B 393 " --> pdb=" O   GLY B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 442
      removed outlier: 3.691A  pdb=" N   GLY B 439 " --> pdb=" O   THR B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 445
      No H-bonds generated for 'chain 'B' and resid 443 through 445'
    Processing helix  chain 'B' and resid 447 through 453
    Processing helix  chain 'B' and resid 460 through 491
      Proline residue:  B 466  - end of helix
      removed outlier: 3.736A  pdb=" N   VAL B 485 " --> pdb=" O   LEU B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 513
    Processing helix  chain 'B' and resid 517 through 550
      removed outlier: 4.396A  pdb=" N   ILE B 521 " --> pdb=" O   SER B 517 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE B 526 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
      Proline residue:  B 541  - end of helix
    Processing helix  chain 'B' and resid 554 through 561
      removed outlier: 3.944A  pdb=" N   VAL B 558 " --> pdb=" O   PHE B 555 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   HIS B 561 " --> pdb=" O   VAL B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 584
      removed outlier: 3.547A  pdb=" N   LEU B 572 " --> pdb=" O   PRO B 568 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU B 573 " --> pdb=" O   THR B 569 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B 574 " --> pdb=" O   TRP B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 616
      Proline residue:  B 593  - end of helix
      removed outlier: 3.828A  pdb=" N   CYS B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 648
      removed outlier: 3.572A  pdb=" N   SER B 633 " --> pdb=" O   HIS B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 675
      removed outlier: 3.631A  pdb=" N   ILE B 653 " --> pdb=" O   TRP B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 696
      removed outlier: 3.585A  pdb=" N   GLU B 696 " --> pdb=" O   LEU B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 734
      removed outlier: 4.293A  pdb=" N   LEU B 726 " --> pdb=" O   HIS B 722 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 752 through 770
    Processing helix  chain 'B' and resid 783 through 795
      removed outlier: 4.034A  pdb=" N   GLN B 793 " --> pdb=" O   SER B 789 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 819 through 835
      removed outlier: 3.598A  pdb=" N   PHE B 825 " --> pdb=" O   ALA B 821 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 844 through 848
    Processing helix  chain 'B' and resid 868 through 881
      removed outlier: 4.055A  pdb=" N   LEU B 872 " --> pdb=" O   ASP B 868 " (cutoff:3.500A)
      Proline residue:  B 876  - end of helix
    Processing helix  chain 'B' and resid 901 through 917
      removed outlier: 3.508A  pdb=" N   ARG B 917 " --> pdb=" O   LEU B 913 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1029 through 1048
      removed outlier: 3.939A  pdb=" N   LYS B1038 " --> pdb=" O   HIS B1034 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1063 through 1065
      No H-bonds generated for 'chain 'B' and resid 1063 through 1065'
    Processing helix  chain 'B' and resid 1066 through 1078
    Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA2, first strand: chain 'A' and resid 342 through 345
      removed outlier: 3.622A  pdb=" N   VAL A 350 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781
      removed outlier: 6.771A  pdb=" N   LEU A 708 " --> pdb=" O   ILE A 740 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   GLY A 742 " --> pdb=" O   LEU A 708 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   VAL A 710 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   VAL A 744 " --> pdb=" O   VAL A 710 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLY A 808 " --> pdb=" O   LEU A 711 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A1084 " --> pdb=" O   LYS A 843 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   VAL A1053 " --> pdb=" O   LEU A1085 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   VAL A1087 " --> pdb=" O   VAL A1053 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LEU A1055 " --> pdb=" O   VAL A1087 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 859 through 860
      removed outlier: 6.691A  pdb=" N   ILE A 890 " --> pdb=" O   GLU A 921 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   GLU A 923 " --> pdb=" O   ILE A 890 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ILE A 892 " --> pdb=" O   GLU A 923 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 345
      removed outlier: 3.622A  pdb=" N   VAL B 350 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 775 through 781
      removed outlier: 6.772A  pdb=" N   LEU B 708 " --> pdb=" O   ILE B 740 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   GLY B 742 " --> pdb=" O   LEU B 708 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   VAL B 710 " --> pdb=" O   GLY B 742 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   VAL B 744 " --> pdb=" O   VAL B 710 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   GLY B 808 " --> pdb=" O   LEU B 711 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B1084 " --> pdb=" O   LYS B 843 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL B1053 " --> pdb=" O   LEU B1085 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B1087 " --> pdb=" O   VAL B1053 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU B1055 " --> pdb=" O   VAL B1087 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 859 through 860
      removed outlier: 6.691A  pdb=" N   ILE B 890 " --> pdb=" O   GLU B 921 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   GLU B 923 " --> pdb=" O   ILE B 890 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ILE B 892 " --> pdb=" O   GLU B 923 " (cutoff:3.500A)

    786 hydrogen bonds defined for protein.
    2262 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: 2.20

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 2945
        1.33 -     1.46: 4321
        1.46 -     1.60: 6050
        1.60 -     1.73: 0
        1.73 -     1.87: 134
  Bond restraints: 13450
  Sorted by residual:
  bond pdb=" N   ILE B 918 "
       pdb=" CA  ILE B 918 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.042 1.14e-02 7.69e+03 1.36e+01
  bond pdb=" N   ILE A 918 "
       pdb=" CA  ILE A 918 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.042 1.14e-02 7.69e+03 1.33e+01
  bond pdb=" C   PHE B 274 "
       pdb=" O   PHE B 274 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.042 1.17e-02 7.31e+03 1.31e+01
  bond pdb=" C   PHE A 274 "
       pdb=" O   PHE A 274 "
    ideal  model  delta    sigma   weight residual
    1.237  1.195  0.042 1.17e-02 7.31e+03 1.30e+01
  bond pdb=" C   ASP B 908 "
       pdb=" O   ASP B 908 "
    ideal  model  delta    sigma   weight residual
    1.237  1.276 -0.040 1.17e-02 7.31e+03 1.15e+01
  ... (remaining 13445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 16977
        1.95 -     3.91: 1136
        3.91 -     5.86: 149
        5.86 -     7.81: 30
        7.81 -     9.77: 12
  Bond angle restraints: 18304
  Sorted by residual:
  angle pdb=" N   GLN A 904 "
        pdb=" CA  GLN A 904 "
        pdb=" C   GLN A 904 "
      ideal   model   delta    sigma   weight residual
     111.28  104.98    6.30 1.09e+00 8.42e-01 3.34e+01
  angle pdb=" N   GLN B 904 "
        pdb=" CA  GLN B 904 "
        pdb=" C   GLN B 904 "
      ideal   model   delta    sigma   weight residual
     111.28  104.99    6.29 1.09e+00 8.42e-01 3.33e+01
  angle pdb=" CA  TRP A 864 "
        pdb=" C   TRP A 864 "
        pdb=" O   TRP A 864 "
      ideal   model   delta    sigma   weight residual
     122.37  116.78    5.59 1.15e+00 7.56e-01 2.37e+01
  angle pdb=" CA  TRP B 864 "
        pdb=" C   TRP B 864 "
        pdb=" O   TRP B 864 "
      ideal   model   delta    sigma   weight residual
     122.37  116.79    5.58 1.15e+00 7.56e-01 2.36e+01
  angle pdb=" C   ILE A 639 "
        pdb=" N   CYS A 640 "
        pdb=" CA  CYS A 640 "
      ideal   model   delta    sigma   weight residual
     122.38  114.41    7.97 1.81e+00 3.05e-01 1.94e+01
  ... (remaining 18299 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.80: 7502
       20.80 -    41.60: 356
       41.60 -    62.40: 72
       62.40 -    83.20: 18
       83.20 -   104.00: 10
  Dihedral angle restraints: 7958
    sinusoidal: 3048
      harmonic: 4910
  Sorted by residual:
  dihedral pdb=" CA  CYS B 640 "
           pdb=" C   CYS B 640 "
           pdb=" N   LEU B 641 "
           pdb=" CA  LEU B 641 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.98   25.02     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  CYS A 640 "
           pdb=" C   CYS A 640 "
           pdb=" N   LEU A 641 "
           pdb=" CA  LEU A 641 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.01   24.99     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CB  CYS A 179 "
           pdb=" SG  CYS A 179 "
           pdb=" SG  CYS A 640 "
           pdb=" CB  CYS A 640 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.58   34.42     1      1.00e+01 1.00e-02 1.68e+01
  ... (remaining 7955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1825
       0.090 -    0.181: 327
       0.181 -    0.271: 20
       0.271 -    0.361: 4
       0.361 -    0.451: 2
  Chirality restraints: 2178
  Sorted by residual:
  chirality pdb=" C1  NAG A1101 "
            pdb=" ND2 ASN A 377 "
            pdb=" C2  NAG A1101 "
            pdb=" O5  NAG A1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.85    0.45 2.00e-01 2.50e+01 5.09e+00
  chirality pdb=" C1  NAG B1101 "
            pdb=" ND2 ASN B 377 "
            pdb=" C2  NAG B1101 "
            pdb=" O5  NAG B1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.85    0.45 2.00e-01 2.50e+01 5.07e+00
  chirality pdb=" CA  CYS B 640 "
            pdb=" N   CYS B 640 "
            pdb=" C   CYS B 640 "
            pdb=" CB  CYS B 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.23e+00
  ... (remaining 2175 not shown)

  Planarity restraints: 2270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 497 "    0.082 9.50e-02 1.11e+02   4.99e-02 1.50e+01
        pdb=" NE  ARG A 497 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 497 "    0.064 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 497 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 497 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 497 "   -0.083 9.50e-02 1.11e+02   5.00e-02 1.49e+01
        pdb=" NE  ARG B 497 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 497 "   -0.064 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 497 "    0.023 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 497 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 240 "   -0.018 2.00e-02 2.50e+03   3.64e-02 1.33e+01
        pdb=" C   PHE B 240 "    0.063 2.00e-02 2.50e+03
        pdb=" O   PHE B 240 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU B 241 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 2267 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3512
        2.80 -     3.32: 13418
        3.32 -     3.85: 21359
        3.85 -     4.37: 24132
        4.37 -     4.90: 41312
  Nonbonded interactions: 103733
  Sorted by model distance:
  nonbonded pdb=" O   THR B 431 "
            pdb=" OG1 THR B 431 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   THR A 431 "
            pdb=" OG1 THR A 431 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   PRO A 698 "
            pdb=" NH1 ARG B 680 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OD1 ASP B 715 "
            pdb=" N   HIS B 719 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OD1 ASP A 715 "
            pdb=" N   HIS A 719 "
     model   vdw
     2.281 3.120
  ... (remaining 103728 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.260
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.890
  Find NCS groups from input model:        0.100
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
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      :  0.010   0.131  13464  Z= 0.486
  Angle     :  1.109  11.546  18340  Z= 0.646
  Chirality :  0.067   0.451   2178
  Planarity :  0.007   0.056   2266
  Dihedral  : 13.737 103.995   4784
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.47 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  6.52 %
    Favored  : 92.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -1.80 (0.18), residues: 1702
  helix: -0.64 (0.15), residues: 954
  sheet: -1.70 (0.46), residues: 92
  loop : -1.81 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.065   0.002   ARG A 497 
 TYR   0.023   0.003   TYR B 222 
 PHE   0.033   0.004   PHE B 441 
 TRP   0.053   0.004   TRP B 822 
 HIS   0.009   0.002   HIS B 790 

Details of bonding type rmsd
  covalent geometry    : bond        0.00972 (13450)
  covalent geometry    : angle       1.07876 (18304)
  SS BOND              : bond        0.01232 (    6)
  SS BOND              : angle       3.16476 (   12)
  hydrogen bonds       : bond        0.12819 (  786)
  hydrogen bonds       : angle       5.73095 ( 2262)
  link_BETA1-4         : bond        0.01423 (    4)
  link_BETA1-4         : angle       5.69836 (   12)
  link_NAG-ASN         : bond        0.10430 (    4)
  link_NAG-ASN         : angle       7.89333 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 277
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  597 MET cc_start: 0.7954 (tpp) cc_final: 0.7707 (tpp)
REVERT: A  601 MET cc_start: 0.8000 (tpp) cc_final: 0.7695 (tpp)
REVERT: A  917 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5372 (mtt180)
REVERT: A  923 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6421 (tm-30)
REVERT: A 1045 ASN cc_start: 0.8242 (m-40) cc_final: 0.7935 (t0)
REVERT: B  263 MET cc_start: 0.7204 (tpp) cc_final: 0.6947 (tpp)
REVERT: B  601 MET cc_start: 0.7882 (tpp) cc_final: 0.7608 (tpp)
REVERT: B  626 ARG cc_start: 0.7003 (ttt-90) cc_final: 0.6582 (tpt170)
REVERT: B  917 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5284 (mtt180)
REVERT: B  923 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6580 (tm-30)
REVERT: B 1081 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6096 (mp)
  outliers start: 8
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1156
  time to fit residues: 47.4170
Evaluate side-chains
  167 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 162
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  917 ARG
Chi-restraints excluded: chain A residue  923 GLU
Chi-restraints excluded: chain B residue  917 ARG
Chi-restraints excluded: chain B residue  923 GLU
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 290 ASN
A 613 GLN
A 731 GLN
A1069 ASN
B 146 GLN
B 290 ASN
B 613 GLN
B 731 GLN
B1069 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.154794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.116241 restraints weight = 18110.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.122258 restraints weight = 8867.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.126511 restraints weight = 5642.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.129411 restraints weight = 4178.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.131515 restraints weight = 3389.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13464  Z= 0.161
  Angle     :  0.662  10.336  18340  Z= 0.336
  Chirality :  0.045   0.261   2178
  Planarity :  0.004   0.050   2266
  Dihedral  :  7.864  54.875   1996
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.45 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.10 (0.20), residues: 1702
  helix:  0.98 (0.16), residues: 934
  sheet: -1.34 (0.49), residues: 92
  loop : -1.35 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 497 
 TYR   0.020   0.001   TYR A 202 
 PHE   0.019   0.002   PHE B 357 
 TRP   0.021   0.002   TRP A 822 
 HIS   0.006   0.001   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (13450)
  covalent geometry    : angle       0.64734 (18304)
  SS BOND              : bond        0.00474 (    6)
  SS BOND              : angle       2.00513 (   12)
  hydrogen bonds       : bond        0.05394 (  786)
  hydrogen bonds       : angle       4.64665 ( 2262)
  link_BETA1-4         : bond        0.00825 (    4)
  link_BETA1-4         : angle       4.08486 (   12)
  link_NAG-ASN         : bond        0.00289 (    4)
  link_NAG-ASN         : angle       3.22221 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.8251 (tpp) cc_final: 0.7865 (tpp)
REVERT: A 1071 MET cc_start: 0.6687 (tpp) cc_final: 0.6406 (tpp)
REVERT: B  263 MET cc_start: 0.7133 (tpp) cc_final: 0.6887 (tpp)
REVERT: B  601 MET cc_start: 0.8166 (tpp) cc_final: 0.7823 (tpp)
REVERT: B  626 ARG cc_start: 0.7339 (ttt-90) cc_final: 0.6484 (tpt170)
REVERT: B  726 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8191 (mm)
REVERT: B  728 PHE cc_start: 0.7593 (t80) cc_final: 0.7246 (t80)
REVERT: B 1057 MET cc_start: 0.6440 (mtp) cc_final: 0.5646 (mtp)
REVERT: B 1071 MET cc_start: 0.6814 (tpp) cc_final: 0.6578 (tpp)
REVERT: B 1081 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6781 (mp)
  outliers start: 24
  outliers final: 9
  residues processed: 232
  average time/residue: 0.0823
  time to fit residues: 31.2675
Evaluate side-chains
  178 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 167
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  743 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain B residue  423 HIS
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  726 LEU
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue 1077 LEU
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 157 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 11 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 129 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 136 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.154318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.115465 restraints weight = 18192.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.121417 restraints weight = 9041.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.125606 restraints weight = 5764.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.128524 restraints weight = 4283.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.130557 restraints weight = 3490.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13464  Z= 0.140
  Angle     :  0.621  10.827  18340  Z= 0.313
  Chirality :  0.045   0.282   2178
  Planarity :  0.004   0.052   2266
  Dihedral  :  6.123  54.009   1982
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.41 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.98 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 (0.20), residues: 1702
  helix:  1.54 (0.17), residues: 934
  sheet: -0.94 (0.52), residues: 92
  loop : -1.24 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1062 
 TYR   0.018   0.001   TYR B 202 
 PHE   0.021   0.001   PHE A 728 
 TRP   0.027   0.002   TRP B 809 
 HIS   0.008   0.001   HIS B 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (13450)
  covalent geometry    : angle       0.60886 (18304)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       2.01218 (   12)
  hydrogen bonds       : bond        0.04910 (  786)
  hydrogen bonds       : angle       4.45959 ( 2262)
  link_BETA1-4         : bond        0.00903 (    4)
  link_BETA1-4         : angle       3.70573 (   12)
  link_NAG-ASN         : bond        0.00350 (    4)
  link_NAG-ASN         : angle       2.64541 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 184
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8240 (m-80) cc_final: 0.7672 (m-80)
REVERT: A  597 MET cc_start: 0.7957 (tpp) cc_final: 0.7566 (tpp)
REVERT: A  601 MET cc_start: 0.8234 (tpp) cc_final: 0.7798 (tpp)
REVERT: A 1071 MET cc_start: 0.7184 (tpp) cc_final: 0.6910 (tpp)
REVERT: B  149 PHE cc_start: 0.8159 (m-80) cc_final: 0.7649 (m-80)
REVERT: B  263 MET cc_start: 0.7200 (tpp) cc_final: 0.6928 (tpp)
REVERT: B  601 MET cc_start: 0.8223 (tpp) cc_final: 0.7812 (tpp)
REVERT: B  626 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.6636 (tpt170)
REVERT: B  726 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8132 (mm)
REVERT: B 1071 MET cc_start: 0.7069 (tpp) cc_final: 0.6844 (tpp)
REVERT: B 1081 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6985 (mp)
  outliers start: 41
  outliers final: 16
  residues processed: 213
  average time/residue: 0.0764
  time to fit residues: 27.2051
Evaluate side-chains
  182 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 164
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  423 HIS
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  726 LEU
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Chi-restraints excluded: chain B residue 1077 LEU
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 149 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 157 optimal weight:    3.9990
   chunk 161 optimal weight:    7.9990
   chunk 21 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 382 GLN
A 765 HIS
B 382 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.152855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.113683 restraints weight = 18389.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.119522 restraints weight = 9167.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.123630 restraints weight = 5897.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.126422 restraints weight = 4401.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.128401 restraints weight = 3613.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13464  Z= 0.143
  Angle     :  0.621  10.778  18340  Z= 0.310
  Chirality :  0.045   0.274   2178
  Planarity :  0.004   0.046   2266
  Dihedral  :  5.529  53.121   1982
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.23 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.96 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.20), residues: 1702
  helix:  1.71 (0.17), residues: 932
  sheet: -0.85 (0.52), residues: 92
  loop : -1.17 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 156 
 TYR   0.014   0.001   TYR A 202 
 PHE   0.016   0.001   PHE A 877 
 TRP   0.016   0.001   TRP B 813 
 HIS   0.007   0.001   HIS A 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (13450)
  covalent geometry    : angle       0.61036 (18304)
  SS BOND              : bond        0.00650 (    6)
  SS BOND              : angle       1.88685 (   12)
  hydrogen bonds       : bond        0.04712 (  786)
  hydrogen bonds       : angle       4.34415 ( 2262)
  link_BETA1-4         : bond        0.00741 (    4)
  link_BETA1-4         : angle       3.43504 (   12)
  link_NAG-ASN         : bond        0.00315 (    4)
  link_NAG-ASN         : angle       2.26090 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 171
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8349 (m-80) cc_final: 0.7719 (m-80)
REVERT: A  601 MET cc_start: 0.8259 (tpp) cc_final: 0.7871 (tpp)
REVERT: A  726 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8227 (mm)
REVERT: A 1071 MET cc_start: 0.7273 (tpp) cc_final: 0.6935 (tpp)
REVERT: B  601 MET cc_start: 0.8205 (tpp) cc_final: 0.7811 (tpp)
REVERT: B  626 ARG cc_start: 0.7362 (ttt-90) cc_final: 0.6621 (tpt170)
REVERT: B  634 PHE cc_start: 0.8778 (t80) cc_final: 0.8251 (t80)
REVERT: B  726 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8166 (mm)
REVERT: B  728 PHE cc_start: 0.7520 (t80) cc_final: 0.7306 (t80)
REVERT: B  743 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7815 (p)
REVERT: B 1071 MET cc_start: 0.7153 (tpp) cc_final: 0.6887 (tpp)
REVERT: B 1081 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7054 (mp)
  outliers start: 30
  outliers final: 16
  residues processed: 193
  average time/residue: 0.0700
  time to fit residues: 22.5874
Evaluate side-chains
  176 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  423 HIS
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  726 LEU
Chi-restraints excluded: chain B residue  743 SER
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 163 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 142 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 153 optimal weight:    7.9990
   chunk 140 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 161 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.149965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.109873 restraints weight = 18606.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.115555 restraints weight = 9280.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.119553 restraints weight = 5997.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.122361 restraints weight = 4503.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.124254 restraints weight = 3713.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13464  Z= 0.150
  Angle     :  0.619   9.779  18340  Z= 0.309
  Chirality :  0.045   0.261   2178
  Planarity :  0.004   0.042   2266
  Dihedral  :  5.193  52.446   1982
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.41 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.72 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.83 (0.21), residues: 1702
  helix:  1.82 (0.17), residues: 926
  sheet: -1.10 (0.49), residues: 96
  loop : -1.00 (0.23), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 156 
 TYR   0.015   0.001   TYR A 202 
 PHE   0.026   0.002   PHE A 728 
 TRP   0.013   0.001   TRP A 813 
 HIS   0.007   0.001   HIS A 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (13450)
  covalent geometry    : angle       0.61017 (18304)
  SS BOND              : bond        0.00626 (    6)
  SS BOND              : angle       1.66563 (   12)
  hydrogen bonds       : bond        0.04630 (  786)
  hydrogen bonds       : angle       4.31388 ( 2262)
  link_BETA1-4         : bond        0.00818 (    4)
  link_BETA1-4         : angle       3.28808 (   12)
  link_NAG-ASN         : bond        0.00248 (    4)
  link_NAG-ASN         : angle       1.97129 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8847 (tpt) cc_final: 0.8586 (tpp)
REVERT: A  280 LEU cc_start: 0.8183 (pp) cc_final: 0.7908 (pp)
REVERT: A  597 MET cc_start: 0.8092 (tpp) cc_final: 0.7809 (tpp)
REVERT: A  601 MET cc_start: 0.8218 (tpp) cc_final: 0.7814 (tpp)
REVERT: A  634 PHE cc_start: 0.8834 (t80) cc_final: 0.8322 (t80)
REVERT: A  726 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8269 (mm)
REVERT: A 1071 MET cc_start: 0.7311 (tpp) cc_final: 0.6887 (tpp)
REVERT: B  263 MET cc_start: 0.7127 (tpp) cc_final: 0.6704 (tpp)
REVERT: B  597 MET cc_start: 0.8078 (tpp) cc_final: 0.7641 (tpp)
REVERT: B  601 MET cc_start: 0.8218 (tpp) cc_final: 0.7753 (tpp)
REVERT: B  626 ARG cc_start: 0.7408 (ttt-90) cc_final: 0.6644 (tpt170)
REVERT: B  638 SER cc_start: 0.8830 (p) cc_final: 0.8414 (p)
REVERT: B  726 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8190 (mm)
REVERT: B  728 PHE cc_start: 0.7681 (t80) cc_final: 0.7366 (t80)
REVERT: B  743 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7725 (p)
REVERT: B 1071 MET cc_start: 0.7205 (tpp) cc_final: 0.6826 (tpp)
REVERT: B 1081 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.6724 (mp)
  outliers start: 30
  outliers final: 14
  residues processed: 195
  average time/residue: 0.0751
  time to fit residues: 24.4799
Evaluate side-chains
  168 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  289 VAL
Chi-restraints excluded: chain B residue  423 HIS
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  726 LEU
Chi-restraints excluded: chain B residue  743 SER
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 156 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 133 optimal weight:    4.9990
   chunk 43 optimal weight:    0.4980
   chunk 29 optimal weight:    5.9990
   chunk 144 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   chunk 143 optimal weight:    0.0970
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 765 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.151025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.110787 restraints weight = 18417.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.116721 restraints weight = 8933.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.120905 restraints weight = 5691.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.123755 restraints weight = 4232.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.125668 restraints weight = 3467.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13464  Z= 0.130
  Angle     :  0.611   9.210  18340  Z= 0.302
  Chirality :  0.044   0.251   2178
  Planarity :  0.004   0.057   2266
  Dihedral  :  5.013  52.883   1982
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.23 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.30 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.96 (0.21), residues: 1702
  helix:  1.95 (0.17), residues: 924
  sheet: -1.11 (0.50), residues: 96
  loop : -0.97 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 814 
 TYR   0.018   0.001   TYR A 202 
 PHE   0.028   0.001   PHE A 728 
 TRP   0.020   0.001   TRP B 813 
 HIS   0.007   0.001   HIS A 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (13450)
  covalent geometry    : angle       0.60229 (18304)
  SS BOND              : bond        0.00940 (    6)
  SS BOND              : angle       1.99748 (   12)
  hydrogen bonds       : bond        0.04473 (  786)
  hydrogen bonds       : angle       4.26157 ( 2262)
  link_BETA1-4         : bond        0.00770 (    4)
  link_BETA1-4         : angle       3.18359 (   12)
  link_NAG-ASN         : bond        0.00250 (    4)
  link_NAG-ASN         : angle       1.95591 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8761 (tpt) cc_final: 0.8500 (tpp)
REVERT: A  280 LEU cc_start: 0.8162 (pp) cc_final: 0.7887 (pp)
REVERT: A  325 MET cc_start: 0.7058 (tpp) cc_final: 0.6626 (tpp)
REVERT: A  601 MET cc_start: 0.8193 (tpp) cc_final: 0.7793 (tpp)
REVERT: A  726 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8214 (mm)
REVERT: A 1071 MET cc_start: 0.7344 (tpp) cc_final: 0.6899 (tpp)
REVERT: B  263 MET cc_start: 0.7166 (tpp) cc_final: 0.6753 (tpp)
REVERT: B  471 LEU cc_start: 0.8684 (mm) cc_final: 0.7523 (tp)
REVERT: B  597 MET cc_start: 0.8031 (tpp) cc_final: 0.7609 (tpp)
REVERT: B  601 MET cc_start: 0.8163 (tpp) cc_final: 0.7786 (tpp)
REVERT: B  626 ARG cc_start: 0.7404 (ttt-90) cc_final: 0.6669 (tpt170)
REVERT: B  634 PHE cc_start: 0.8763 (t80) cc_final: 0.8544 (t80)
REVERT: B  726 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8117 (mm)
REVERT: B  728 PHE cc_start: 0.7718 (t80) cc_final: 0.7397 (t80)
REVERT: B  743 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7573 (p)
REVERT: B 1071 MET cc_start: 0.7314 (tpp) cc_final: 0.6936 (tpp)
REVERT: B 1081 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6537 (mp)
  outliers start: 26
  outliers final: 11
  residues processed: 192
  average time/residue: 0.0758
  time to fit residues: 24.0415
Evaluate side-chains
  172 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  726 LEU
Chi-restraints excluded: chain B residue  743 SER
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 156 optimal weight:    3.9990
   chunk 119 optimal weight:    0.6980
   chunk 126 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 130 optimal weight:    4.9990
   chunk 169 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 159 optimal weight:    0.7980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.152661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.113564 restraints weight = 18569.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.119360 restraints weight = 9234.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.123488 restraints weight = 5925.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.126255 restraints weight = 4412.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.128119 restraints weight = 3611.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13464  Z= 0.133
  Angle     :  0.612   9.377  18340  Z= 0.303
  Chirality :  0.044   0.281   2178
  Planarity :  0.004   0.059   2266
  Dihedral  :  4.927  52.905   1982
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.47 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.59 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  0.96 (0.21), residues: 1702
  helix:  1.94 (0.17), residues: 924
  sheet: -1.15 (0.50), residues: 96
  loop : -0.95 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 814 
 TYR   0.016   0.001   TYR A 202 
 PHE   0.028   0.001   PHE A 728 
 TRP   0.032   0.001   TRP A 813 
 HIS   0.009   0.001   HIS A 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (13450)
  covalent geometry    : angle       0.60248 (18304)
  SS BOND              : bond        0.00813 (    6)
  SS BOND              : angle       2.22880 (   12)
  hydrogen bonds       : bond        0.04469 (  786)
  hydrogen bonds       : angle       4.32548 ( 2262)
  link_BETA1-4         : bond        0.00627 (    4)
  link_BETA1-4         : angle       3.13299 (   12)
  link_NAG-ASN         : bond        0.00219 (    4)
  link_NAG-ASN         : angle       1.86992 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8679 (tpt) cc_final: 0.8424 (tpp)
REVERT: A  280 LEU cc_start: 0.8172 (pp) cc_final: 0.7890 (pp)
REVERT: A  325 MET cc_start: 0.6911 (tpp) cc_final: 0.6484 (tpp)
REVERT: A  601 MET cc_start: 0.8169 (tpp) cc_final: 0.7762 (tpp)
REVERT: A  726 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8280 (mm)
REVERT: A 1071 MET cc_start: 0.7498 (tpp) cc_final: 0.6981 (tpp)
REVERT: B  263 MET cc_start: 0.7182 (tpp) cc_final: 0.6789 (tpp)
REVERT: B  280 LEU cc_start: 0.8076 (pp) cc_final: 0.7798 (pp)
REVERT: B  597 MET cc_start: 0.7977 (tpp) cc_final: 0.7661 (tpp)
REVERT: B  601 MET cc_start: 0.8147 (tpp) cc_final: 0.7741 (tpp)
REVERT: B  626 ARG cc_start: 0.7434 (ttt-90) cc_final: 0.6712 (tpt170)
REVERT: B  743 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7610 (p)
REVERT: B 1071 MET cc_start: 0.7378 (tpp) cc_final: 0.6978 (tpp)
  outliers start: 24
  outliers final: 14
  residues processed: 191
  average time/residue: 0.0740
  time to fit residues: 23.5028
Evaluate side-chains
  180 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  627 TYR
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  743 SER
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 160 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 156 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4208 r_free = 0.4208 target = 0.152743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.113843 restraints weight = 18238.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.119633 restraints weight = 9127.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.123689 restraints weight = 5864.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.126431 restraints weight = 4372.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.128394 restraints weight = 3578.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13464  Z= 0.139
  Angle     :  0.614   8.843  18340  Z= 0.307
  Chirality :  0.045   0.266   2178
  Planarity :  0.004   0.060   2266
  Dihedral  :  4.787  52.992   1980
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.70 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 18.81 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.94 (0.21), residues: 1702
  helix:  1.93 (0.17), residues: 924
  sheet: -1.30 (0.47), residues: 104
  loop : -0.93 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 917 
 TYR   0.016   0.001   TYR A 202 
 PHE   0.025   0.001   PHE A 728 
 TRP   0.033   0.002   TRP A 813 
 HIS   0.011   0.001   HIS B 915 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (13450)
  covalent geometry    : angle       0.60525 (18304)
  SS BOND              : bond        0.00735 (    6)
  SS BOND              : angle       2.17283 (   12)
  hydrogen bonds       : bond        0.04453 (  786)
  hydrogen bonds       : angle       4.34244 ( 2262)
  link_BETA1-4         : bond        0.00636 (    4)
  link_BETA1-4         : angle       3.12477 (   12)
  link_NAG-ASN         : bond        0.00200 (    4)
  link_NAG-ASN         : angle       1.78538 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8634 (tpt) cc_final: 0.8381 (tpp)
REVERT: A  280 LEU cc_start: 0.8186 (pp) cc_final: 0.7903 (pp)
REVERT: A  325 MET cc_start: 0.6726 (tpp) cc_final: 0.6290 (tpp)
REVERT: A  601 MET cc_start: 0.8153 (tpp) cc_final: 0.7767 (tpp)
REVERT: A  726 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8362 (mm)
REVERT: A 1071 MET cc_start: 0.7503 (tpp) cc_final: 0.6981 (tpp)
REVERT: B  181 MET cc_start: 0.8656 (tpt) cc_final: 0.8344 (tpp)
REVERT: B  263 MET cc_start: 0.7088 (tpp) cc_final: 0.6649 (tpp)
REVERT: B  280 LEU cc_start: 0.8092 (pp) cc_final: 0.7812 (pp)
REVERT: B  471 LEU cc_start: 0.8707 (mm) cc_final: 0.7478 (tp)
REVERT: B  597 MET cc_start: 0.7975 (tpp) cc_final: 0.7587 (tpp)
REVERT: B  601 MET cc_start: 0.8119 (tpp) cc_final: 0.7679 (tpp)
REVERT: B  626 ARG cc_start: 0.7416 (ttt-90) cc_final: 0.6875 (tpt170)
REVERT: B  743 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7566 (p)
REVERT: B 1071 MET cc_start: 0.7452 (tpp) cc_final: 0.7049 (tpp)
REVERT: B 1081 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6652 (mp)
  outliers start: 23
  outliers final: 14
  residues processed: 189
  average time/residue: 0.0736
  time to fit residues: 23.4915
Evaluate side-chains
  183 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  627 TYR
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  743 SER
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 160 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 119 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 147 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.154987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.115914 restraints weight = 18245.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.121845 restraints weight = 9018.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.125992 restraints weight = 5741.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.128762 restraints weight = 4262.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.130660 restraints weight = 3481.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13464  Z= 0.126
  Angle     :  0.605   8.555  18340  Z= 0.300
  Chirality :  0.044   0.255   2178
  Planarity :  0.004   0.062   2266
  Dihedral  :  4.701  53.470   1980
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.29 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 19.25 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.03 (0.21), residues: 1702
  helix:  2.02 (0.17), residues: 924
  sheet: -1.20 (0.47), residues: 104
  loop : -0.92 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 917 
 TYR   0.016   0.001   TYR A 202 
 PHE   0.027   0.001   PHE A 728 
 TRP   0.037   0.002   TRP A 813 
 HIS   0.004   0.001   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13450)
  covalent geometry    : angle       0.59701 (18304)
  SS BOND              : bond        0.00593 (    6)
  SS BOND              : angle       1.92731 (   12)
  hydrogen bonds       : bond        0.04320 (  786)
  hydrogen bonds       : angle       4.29383 ( 2262)
  link_BETA1-4         : bond        0.00670 (    4)
  link_BETA1-4         : angle       3.02495 (   12)
  link_NAG-ASN         : bond        0.00188 (    4)
  link_NAG-ASN         : angle       1.76658 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8629 (tpt) cc_final: 0.8371 (tpp)
REVERT: A  280 LEU cc_start: 0.8187 (pp) cc_final: 0.7908 (pp)
REVERT: A  325 MET cc_start: 0.6682 (tpp) cc_final: 0.6255 (tpp)
REVERT: A  601 MET cc_start: 0.8157 (tpp) cc_final: 0.7802 (tpp)
REVERT: A  726 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8225 (mm)
REVERT: A 1071 MET cc_start: 0.7511 (tpp) cc_final: 0.6928 (tpp)
REVERT: B  263 MET cc_start: 0.7103 (tpp) cc_final: 0.6696 (tpp)
REVERT: B  280 LEU cc_start: 0.8094 (pp) cc_final: 0.7818 (pp)
REVERT: B  471 LEU cc_start: 0.8681 (mm) cc_final: 0.7445 (tp)
REVERT: B  597 MET cc_start: 0.8057 (tpp) cc_final: 0.7725 (tpp)
REVERT: B  601 MET cc_start: 0.8040 (tpp) cc_final: 0.7635 (tpp)
REVERT: B  626 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.6887 (tpt170)
REVERT: B  743 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7481 (p)
REVERT: B 1071 MET cc_start: 0.7505 (tpp) cc_final: 0.7090 (tpp)
  outliers start: 20
  outliers final: 13
  residues processed: 183
  average time/residue: 0.0766
  time to fit residues: 23.5537
Evaluate side-chains
  175 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  627 TYR
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  743 SER
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 166 optimal weight:    2.9990
   chunk 141 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 127 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 124 optimal weight:    0.7980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.154518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.115504 restraints weight = 18111.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.121330 restraints weight = 9015.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.125434 restraints weight = 5767.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.128171 restraints weight = 4286.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.130067 restraints weight = 3502.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13464  Z= 0.133
  Angle     :  0.615   8.245  18340  Z= 0.306
  Chirality :  0.044   0.259   2178
  Planarity :  0.004   0.058   2266
  Dihedral  :  4.665  53.518   1980
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.41 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 19.40 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.06 (0.21), residues: 1702
  helix:  2.01 (0.17), residues: 928
  sheet: -1.20 (0.48), residues: 104
  loop : -0.88 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 917 
 TYR   0.016   0.001   TYR A 202 
 PHE   0.026   0.001   PHE A 728 
 TRP   0.039   0.002   TRP A 813 
 HIS   0.005   0.001   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (13450)
  covalent geometry    : angle       0.60709 (18304)
  SS BOND              : bond        0.00617 (    6)
  SS BOND              : angle       1.94345 (   12)
  hydrogen bonds       : bond        0.04316 (  786)
  hydrogen bonds       : angle       4.29080 ( 2262)
  link_BETA1-4         : bond        0.00661 (    4)
  link_BETA1-4         : angle       2.99446 (   12)
  link_NAG-ASN         : bond        0.00164 (    4)
  link_NAG-ASN         : angle       1.68980 (   12)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8603 (tpt) cc_final: 0.8345 (tpp)
REVERT: A  280 LEU cc_start: 0.8203 (pp) cc_final: 0.7926 (pp)
REVERT: A  325 MET cc_start: 0.6810 (tpp) cc_final: 0.6330 (mmt)
REVERT: A  601 MET cc_start: 0.8110 (tpp) cc_final: 0.7711 (tpp)
REVERT: A  726 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8270 (mm)
REVERT: A 1071 MET cc_start: 0.7530 (tpp) cc_final: 0.7198 (tpp)
REVERT: B  238 GLU cc_start: 0.7081 (tp30) cc_final: 0.6863 (tt0)
REVERT: B  263 MET cc_start: 0.7069 (tpp) cc_final: 0.6614 (tpp)
REVERT: B  280 LEU cc_start: 0.8113 (pp) cc_final: 0.7837 (pp)
REVERT: B  597 MET cc_start: 0.8032 (tpp) cc_final: 0.7676 (tpp)
REVERT: B  601 MET cc_start: 0.8005 (tpp) cc_final: 0.7582 (tpp)
REVERT: B  626 ARG cc_start: 0.7459 (ttt-90) cc_final: 0.6809 (tpt90)
REVERT: B  743 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7501 (p)
REVERT: B 1071 MET cc_start: 0.7461 (tpp) cc_final: 0.7113 (tpp)
REVERT: B 1081 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.6690 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 175
  average time/residue: 0.0752
  time to fit residues: 22.1646
Evaluate side-chains
  176 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  627 TYR
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  726 LEU
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  800 MET
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  726 LEU
Chi-restraints excluded: chain B residue  743 SER
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  778 LEU
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 145 optimal weight:    4.9990
   chunk 168 optimal weight:    0.9980
   chunk 138 optimal weight:    2.9990
   chunk 156 optimal weight:    0.6980
   chunk 105 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 119 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 133 optimal weight:    0.0570
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
B 882 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.158864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.120591 restraints weight = 17623.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.126425 restraints weight = 8913.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.130547 restraints weight = 5728.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.133281 restraints weight = 4249.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.135194 restraints weight = 3463.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13464  Z= 0.116
  Angle     :  0.601   8.518  18340  Z= 0.296
  Chirality :  0.043   0.249   2178
  Planarity :  0.004   0.056   2266
  Dihedral  :  4.562  54.200   1980
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 19.62 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.21 (0.21), residues: 1702
  helix:  2.08 (0.17), residues: 934
  sheet: -1.02 (0.49), residues: 104
  loop : -0.77 (0.25), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1088 
 TYR   0.015   0.001   TYR A 202 
 PHE   0.029   0.001   PHE A 728 
 TRP   0.040   0.002   TRP A 813 
 HIS   0.005   0.001   HIS B 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13450)
  covalent geometry    : angle       0.59359 (18304)
  SS BOND              : bond        0.00552 (    6)
  SS BOND              : angle       1.75925 (   12)
  hydrogen bonds       : bond        0.04098 (  786)
  hydrogen bonds       : angle       4.22006 ( 2262)
  link_BETA1-4         : bond        0.00642 (    4)
  link_BETA1-4         : angle       2.91377 (   12)
  link_NAG-ASN         : bond        0.00186 (    4)
  link_NAG-ASN         : angle       1.71043 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2442.02 seconds
wall clock time: 42 minutes 43.60 seconds (2563.60 seconds total)