Starting phenix.real_space_refine
on Thu Jul 31 08:02:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ngb_12311/07_2025/7ngb_12311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ngb_12311/07_2025/7ngb_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2025/7ngb_12311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2025/7ngb_12311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2025/7ngb_12311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ngb_12311/07_2025/7ngb_12311.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 6, 'ARG: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: 14.51, per 1000 atoms: 1.10
  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: 3.30
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 1.42
  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: 4.37

  Time building geometry restraints manager: 3.96 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: 0.07
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:             3.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     39.080
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.100
-------------------------------------------------------------------------------
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 : 13.40
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.053   0.004   TRP B 822 
 HIS   0.009   0.002   HIS B 790 
 PHE   0.033   0.004   PHE B 441 
 TYR   0.023   0.003   TYR B 222 
 ARG   0.065   0.002   ARG A 497 

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

*********************** 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  : 1.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.8000 (tpp) cc_final: 0.7644 (tpp)
REVERT: A  917 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5372 (mtt180)
REVERT: A  923 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6420 (tm-30)
REVERT: A 1045 ASN cc_start: 0.8242 (m-40) cc_final: 0.7938 (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: 0.6581 (tpt170)
REVERT: B  917 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5283 (mtt180)
REVERT: B  923 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6580 (tm-30)
REVERT: B 1081 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6097 (mp)
  outliers start: 8
  outliers final: 0
  residues processed: 281
  average time/residue: 0.2564
  time to fit residues: 104.7064
Evaluate side-chains
  166 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 161
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
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 143 optimal weight:    0.0070
   chunk 128 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 154 optimal weight:    0.8980
   overall best weight:    0.6600

-------------------------------------------------------------------------------
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 = 0.4279 r_free = 0.4279 target = 0.158892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.118613 restraints weight = 17795.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.125220 restraints weight = 8321.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.129769 restraints weight = 5190.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13464  Z= 0.152
  Angle     :  0.663  10.360  18340  Z= 0.334
  Chirality :  0.045   0.249   2178
  Planarity :  0.004   0.050   2266
  Dihedral  :  7.780  54.963   1996
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.59 %
    Favored  : 85.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.20), residues: 1702
  helix:  1.02 (0.16), residues: 934
  sheet: -1.25 (0.49), residues: 92
  loop : -1.37 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 822 
 HIS   0.007   0.001   HIS B 423 
 PHE   0.021   0.002   PHE B 357 
 TYR   0.020   0.001   TYR B 202 
 ARG   0.007   0.001   ARG A 497 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00627 (    4)
  link_NAG-ASN         : angle       3.19916 (   12)
  link_BETA1-4         : bond        0.00754 (    4)
  link_BETA1-4         : angle       4.06422 (   12)
  hydrogen bonds       : bond        0.05268 (  786)
  hydrogen bonds       : angle       4.60902 ( 2262)
  SS BOND              : bond        0.00425 (    6)
  SS BOND              : angle       2.10882 (   12)
  covalent geometry    : bond        0.00331 (13450)
  covalent geometry    : angle       0.64777 (18304)

*********************** 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
  241 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 218
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.8266 (tpp) cc_final: 0.7835 (tpp)
REVERT: A  917 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5461 (mmt90)
REVERT: A 1045 ASN cc_start: 0.8726 (m-40) cc_final: 0.8325 (t0)
REVERT: B  263 MET cc_start: 0.7122 (tpp) cc_final: 0.6900 (tpp)
REVERT: B  601 MET cc_start: 0.8214 (tpp) cc_final: 0.7868 (tpp)
REVERT: B  626 ARG cc_start: 0.7364 (ttt-90) cc_final: 0.6443 (tpt170)
REVERT: B  728 PHE cc_start: 0.7624 (t80) cc_final: 0.7356 (t80)
REVERT: B 1057 MET cc_start: 0.6421 (mtp) cc_final: 0.5624 (mtp)
REVERT: B 1071 MET cc_start: 0.6850 (tpp) cc_final: 0.6598 (tpp)
REVERT: B 1081 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6850 (mp)
  outliers start: 23
  outliers final: 7
  residues processed: 235
  average time/residue: 0.1935
  time to fit residues: 73.0871
Evaluate side-chains
  175 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 166
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  743 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  917 ARG
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  788 ILE
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 134 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 142 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4206 r_free = 0.4206 target = 0.152556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.113564 restraints weight = 18399.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.119287 restraints weight = 9212.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.123387 restraints weight = 5924.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  13464  Z= 0.172
  Angle     :  0.656  10.068  18340  Z= 0.329
  Chirality :  0.046   0.300   2178
  Planarity :  0.004   0.052   2266
  Dihedral  :  6.357  53.951   1986
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.58 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.49 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.20), residues: 1702
  helix:  1.41 (0.17), residues: 934
  sheet: -1.05 (0.52), residues: 92
  loop : -1.28 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 809 
 HIS   0.008   0.001   HIS B 915 
 PHE   0.019   0.002   PHE A 728 
 TYR   0.019   0.002   TYR A 202 
 ARG   0.003   0.000   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    4)
  link_NAG-ASN         : angle       2.66212 (   12)
  link_BETA1-4         : bond        0.00659 (    4)
  link_BETA1-4         : angle       3.78448 (   12)
  hydrogen bonds       : bond        0.05062 (  786)
  hydrogen bonds       : angle       4.55217 ( 2262)
  SS BOND              : bond        0.01398 (    6)
  SS BOND              : angle       2.79899 (   12)
  covalent geometry    : bond        0.00406 (13450)
  covalent geometry    : angle       0.64180 (18304)

*********************** 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
  223 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 182
  time to evaluate  : 2.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8176 (m-80) cc_final: 0.7714 (m-80)
REVERT: A  601 MET cc_start: 0.8267 (tpp) cc_final: 0.7798 (tpp)
REVERT: A 1045 ASN cc_start: 0.8646 (m-40) cc_final: 0.8304 (t0)
REVERT: B  149 PHE cc_start: 0.8148 (m-80) cc_final: 0.7709 (m-80)
REVERT: B  263 MET cc_start: 0.7179 (tpp) cc_final: 0.6896 (tpp)
REVERT: B  601 MET cc_start: 0.8251 (tpp) cc_final: 0.7855 (tpp)
REVERT: B  626 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.6630 (tpt170)
REVERT: B  743 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.7994 (p)
REVERT: B 1071 MET cc_start: 0.7131 (tpp) cc_final: 0.6907 (tpp)
REVERT: B 1081 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7038 (mp)
  outliers start: 41
  outliers final: 18
  residues processed: 210
  average time/residue: 0.1793
  time to fit residues: 61.3686
Evaluate side-chains
  184 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 1.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 MET
Chi-restraints excluded: chain A residue  148 ILE
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 A residue  829 VAL
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 160 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 80 optimal weight:    0.7980
   chunk 132 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 133 optimal weight:    0.0050
   chunk 131 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 127 optimal weight:    0.2980
   overall best weight:    0.4594

-------------------------------------------------------------------------------
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 = 0.4264 r_free = 0.4264 target = 0.158108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.119193 restraints weight = 17739.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.125271 restraints weight = 8720.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.129531 restraints weight = 5519.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13464  Z= 0.123
  Angle     :  0.612  10.691  18340  Z= 0.303
  Chirality :  0.044   0.265   2178
  Planarity :  0.004   0.046   2266
  Dihedral  :  5.489  53.749   1982
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.94 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.69 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.20), residues: 1702
  helix:  1.73 (0.17), residues: 926
  sheet: -0.82 (0.52), residues: 92
  loop : -1.10 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 813 
 HIS   0.008   0.001   HIS A 915 
 PHE   0.018   0.001   PHE A 877 
 TYR   0.020   0.001   TYR A 202 
 ARG   0.002   0.000   ARG B 626 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00340 (    4)
  link_NAG-ASN         : angle       2.33838 (   12)
  link_BETA1-4         : bond        0.00600 (    4)
  link_BETA1-4         : angle       3.40310 (   12)
  hydrogen bonds       : bond        0.04583 (  786)
  hydrogen bonds       : angle       4.32156 ( 2262)
  SS BOND              : bond        0.00654 (    6)
  SS BOND              : angle       1.96740 (   12)
  covalent geometry    : bond        0.00260 (13450)
  covalent geometry    : angle       0.60121 (18304)

*********************** 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
  204 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8232 (m-80) cc_final: 0.7701 (m-80)
REVERT: A  601 MET cc_start: 0.8262 (tpp) cc_final: 0.7875 (tpp)
REVERT: A  726 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8185 (mm)
REVERT: B  149 PHE cc_start: 0.8267 (m-80) cc_final: 0.7758 (m-80)
REVERT: B  601 MET cc_start: 0.8200 (tpp) cc_final: 0.7784 (tpp)
REVERT: B  626 ARG cc_start: 0.7340 (ttt-90) cc_final: 0.6599 (tpt170)
REVERT: B  728 PHE cc_start: 0.7481 (t80) cc_final: 0.7245 (t80)
REVERT: B 1071 MET cc_start: 0.7206 (tpp) cc_final: 0.6898 (tpp)
REVERT: B 1081 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7030 (mp)
  outliers start: 25
  outliers final: 11
  residues processed: 200
  average time/residue: 0.1804
  time to fit residues: 59.3563
Evaluate side-chains
  175 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ILE
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  148 ILE
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  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 45 optimal weight:    4.9990
   chunk 131 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 153 optimal weight:    0.0770
   chunk 125 optimal weight:    0.8980
   chunk 61 optimal weight:    0.1980
   chunk 157 optimal weight:   10.0000
   chunk 162 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 150 optimal weight:    2.9990
   overall best weight:    0.6340

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.153810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.113309 restraints weight = 18322.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.119447 restraints weight = 8810.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.123709 restraints weight = 5574.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3079

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= 0.121
  Angle     :  0.588   9.620  18340  Z= 0.293
  Chirality :  0.044   0.249   2178
  Planarity :  0.004   0.043   2266
  Dihedral  :  5.144  52.958   1982
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.28 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.20), residues: 1702
  helix:  1.91 (0.17), residues: 926
  sheet: -0.76 (0.51), residues: 92
  loop : -0.95 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 813 
 HIS   0.007   0.001   HIS A 915 
 PHE   0.030   0.001   PHE A 728 
 TYR   0.018   0.001   TYR A 202 
 ARG   0.002   0.000   ARG B 724 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00286 (    4)
  link_NAG-ASN         : angle       2.09463 (   12)
  link_BETA1-4         : bond        0.00632 (    4)
  link_BETA1-4         : angle       3.25751 (   12)
  hydrogen bonds       : bond        0.04414 (  786)
  hydrogen bonds       : angle       4.21868 ( 2262)
  SS BOND              : bond        0.00370 (    6)
  SS BOND              : angle       1.82088 (   12)
  covalent geometry    : bond        0.00262 (13450)
  covalent geometry    : angle       0.57845 (18304)

*********************** 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
  212 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 180
  time to evaluate  : 1.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8283 (m-80) cc_final: 0.7743 (m-80)
REVERT: A  601 MET cc_start: 0.8228 (tpp) cc_final: 0.7804 (tpp)
REVERT: A  644 MET cc_start: 0.8128 (ttm) cc_final: 0.7878 (ttp)
REVERT: A  726 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8227 (mm)
REVERT: B  263 MET cc_start: 0.7220 (tpp) cc_final: 0.6761 (tpp)
REVERT: B  601 MET cc_start: 0.8227 (tpp) cc_final: 0.7804 (tpp)
REVERT: B  626 ARG cc_start: 0.7368 (ttt-90) cc_final: 0.6597 (tpt170)
REVERT: B  728 PHE cc_start: 0.7656 (t80) cc_final: 0.7421 (t80)
REVERT: B  826 ILE cc_start: 0.7685 (pt) cc_final: 0.7415 (pt)
REVERT: B 1071 MET cc_start: 0.7271 (tpp) cc_final: 0.6909 (tpp)
  outliers start: 32
  outliers final: 15
  residues processed: 207
  average time/residue: 0.1782
  time to fit residues: 60.5742
Evaluate side-chains
  177 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ILE
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  148 ILE
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  573 LEU
Chi-restraints excluded: chain B residue  720 VAL
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:   20.0000
   chunk 167 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 152 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 166 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0470
   overall best weight:    1.0880

-------------------------------------------------------------------------------
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 = 0.4209 r_free = 0.4209 target = 0.152437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.113323 restraints weight = 18776.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.119165 restraints weight = 9309.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.123271 restraints weight = 5977.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.3218

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= 0.143
  Angle     :  0.618   9.337  18340  Z= 0.309
  Chirality :  0.044   0.276   2178
  Planarity :  0.004   0.057   2266
  Dihedral  :  4.947  52.719   1980
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.35 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.08 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.21), residues: 1702
  helix:  1.93 (0.17), residues: 924
  sheet: -0.95 (0.50), residues: 92
  loop : -0.89 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 813 
 HIS   0.005   0.001   HIS B 423 
 PHE   0.027   0.002   PHE A 728 
 TYR   0.016   0.001   TYR B 202 
 ARG   0.003   0.000   ARG A 814 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    4)
  link_NAG-ASN         : angle       1.95047 (   12)
  link_BETA1-4         : bond        0.00617 (    4)
  link_BETA1-4         : angle       3.21733 (   12)
  hydrogen bonds       : bond        0.04506 (  786)
  hydrogen bonds       : angle       4.34893 ( 2262)
  SS BOND              : bond        0.00685 (    6)
  SS BOND              : angle       2.18718 (   12)
  covalent geometry    : bond        0.00325 (13450)
  covalent geometry    : angle       0.60870 (18304)

*********************** 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
  192 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8729 (tpt) cc_final: 0.8490 (tpp)
REVERT: A  280 LEU cc_start: 0.8192 (pp) cc_final: 0.7924 (pp)
REVERT: A  601 MET cc_start: 0.8225 (tpp) cc_final: 0.7797 (tpp)
REVERT: A  644 MET cc_start: 0.8152 (ttm) cc_final: 0.7935 (ttp)
REVERT: A  726 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8295 (mm)
REVERT: B  181 MET cc_start: 0.8684 (tpt) cc_final: 0.8410 (tpp)
REVERT: B  263 MET cc_start: 0.7153 (tpp) cc_final: 0.6747 (tpp)
REVERT: B  601 MET cc_start: 0.8206 (tpp) cc_final: 0.7767 (tpp)
REVERT: B  626 ARG cc_start: 0.7356 (ttt-90) cc_final: 0.6668 (tpt170)
REVERT: B  874 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7997 (tt)
REVERT: B 1071 MET cc_start: 0.7343 (tpp) cc_final: 0.6924 (tpp)
  outliers start: 21
  outliers final: 13
  residues processed: 189
  average time/residue: 0.1720
  time to fit residues: 54.1349
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  : 1.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  423 HIS
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  788 ILE
Chi-restraints excluded: chain B residue  800 MET
Chi-restraints excluded: chain B residue  874 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 150 optimal weight:    3.9990
   chunk 167 optimal weight:    0.5980
   chunk 130 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0970
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.4247 r_free = 0.4247 target = 0.156203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.117238 restraints weight = 18177.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.123274 restraints weight = 8888.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.127520 restraints weight = 5635.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  13464  Z= 0.123
  Angle     :  0.606   8.961  18340  Z= 0.301
  Chirality :  0.044   0.284   2178
  Planarity :  0.004   0.058   2266
  Dihedral  :  4.831  53.052   1980
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 18.30 %
    Favored  : 80.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.21), residues: 1702
  helix:  1.96 (0.17), residues: 928
  sheet: -1.02 (0.49), residues: 96
  loop : -0.87 (0.24), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 813 
 HIS   0.006   0.001   HIS B 915 
 PHE   0.022   0.001   PHE A 728 
 TYR   0.016   0.001   TYR B 202 
 ARG   0.002   0.000   ARG A 814 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00247 (    4)
  link_NAG-ASN         : angle       1.91448 (   12)
  link_BETA1-4         : bond        0.00592 (    4)
  link_BETA1-4         : angle       3.09777 (   12)
  hydrogen bonds       : bond        0.04399 (  786)
  hydrogen bonds       : angle       4.32615 ( 2262)
  SS BOND              : bond        0.00840 (    6)
  SS BOND              : angle       2.27405 (   12)
  covalent geometry    : bond        0.00272 (13450)
  covalent geometry    : angle       0.59637 (18304)

*********************** 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
  196 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8685 (tpt) cc_final: 0.8459 (tpp)
REVERT: A  280 LEU cc_start: 0.8190 (pp) cc_final: 0.7923 (pp)
REVERT: A  601 MET cc_start: 0.8160 (tpp) cc_final: 0.7765 (tpp)
REVERT: A  726 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8243 (mm)
REVERT: B  181 MET cc_start: 0.8619 (tpt) cc_final: 0.8355 (tpp)
REVERT: B  263 MET cc_start: 0.7149 (tpp) cc_final: 0.6751 (tpp)
REVERT: B  471 LEU cc_start: 0.8766 (mm) cc_final: 0.7672 (tp)
REVERT: B  597 MET cc_start: 0.8026 (mmm) cc_final: 0.7784 (mmm)
REVERT: B  601 MET cc_start: 0.8170 (tpp) cc_final: 0.7718 (tpp)
REVERT: B  626 ARG cc_start: 0.7362 (ttt-90) cc_final: 0.6666 (tpt170)
REVERT: B  728 PHE cc_start: 0.7453 (t80) cc_final: 0.7233 (t80)
REVERT: B  874 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8107 (tt)
REVERT: B 1071 MET cc_start: 0.7453 (tpp) cc_final: 0.7034 (tpp)
REVERT: B 1081 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7105 (mp)
  outliers start: 23
  outliers final: 15
  residues processed: 190
  average time/residue: 0.1882
  time to fit residues: 59.2303
Evaluate side-chains
  183 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
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 A residue 1067 ASP
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  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  874 LEU
Chi-restraints excluded: chain B residue 1081 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 128 optimal weight:    5.9990
   chunk 163 optimal weight:    0.0370
   chunk 113 optimal weight:   20.0000
   chunk 129 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 90 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0970
   overall best weight:    0.4656

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.158081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.119202 restraints weight = 17964.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.125360 restraints weight = 8703.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.129635 restraints weight = 5490.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13464  Z= 0.117
  Angle     :  0.603  14.706  18340  Z= 0.297
  Chirality :  0.044   0.262   2178
  Planarity :  0.004   0.059   2266
  Dihedral  :  4.690  53.269   1980
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.88 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.81 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.21), residues: 1702
  helix:  2.04 (0.17), residues: 936
  sheet: -0.69 (0.52), residues: 92
  loop : -0.81 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 813 
 HIS   0.006   0.001   HIS B 915 
 PHE   0.024   0.001   PHE B 487 
 TYR   0.014   0.001   TYR B 202 
 ARG   0.002   0.000   ARG A 814 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    4)
  link_NAG-ASN         : angle       1.85986 (   12)
  link_BETA1-4         : bond        0.00613 (    4)
  link_BETA1-4         : angle       3.03920 (   12)
  hydrogen bonds       : bond        0.04241 (  786)
  hydrogen bonds       : angle       4.28407 ( 2262)
  SS BOND              : bond        0.00634 (    6)
  SS BOND              : angle       1.92287 (   12)
  covalent geometry    : bond        0.00250 (13450)
  covalent geometry    : angle       0.59436 (18304)

*********************** 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
  192 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 172
  time to evaluate  : 1.682 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8690 (tpt) cc_final: 0.8454 (tpp)
REVERT: A  471 LEU cc_start: 0.8732 (mm) cc_final: 0.7554 (tp)
REVERT: A  601 MET cc_start: 0.8160 (tpp) cc_final: 0.7781 (tpp)
REVERT: A  726 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8229 (mm)
REVERT: B  181 MET cc_start: 0.8628 (tpt) cc_final: 0.8365 (tpp)
REVERT: B  263 MET cc_start: 0.7157 (tpp) cc_final: 0.6789 (tpp)
REVERT: B  471 LEU cc_start: 0.8689 (mm) cc_final: 0.7504 (tp)
REVERT: B  601 MET cc_start: 0.8139 (tpp) cc_final: 0.7708 (tpp)
REVERT: B  626 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.6646 (tpt170)
REVERT: B  728 PHE cc_start: 0.7500 (t80) cc_final: 0.7264 (t80)
REVERT: B 1071 MET cc_start: 0.7465 (tpp) cc_final: 0.7101 (tpp)
REVERT: B 1081 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7155 (mp)
  outliers start: 20
  outliers final: 14
  residues processed: 185
  average time/residue: 0.2668
  time to fit residues: 81.3504
Evaluate side-chains
  174 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 148 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 164 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   chunk 141 optimal weight:    2.9990
   chunk 155 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   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 = 0.4240 r_free = 0.4240 target = 0.155192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.116369 restraints weight = 18169.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.122328 restraints weight = 8949.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.126494 restraints weight = 5687.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13464  Z= 0.135
  Angle     :  0.639  16.066  18340  Z= 0.313
  Chirality :  0.044   0.259   2178
  Planarity :  0.004   0.058   2266
  Dihedral  :  4.677  53.007   1980
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 19.47 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.21), residues: 1702
  helix:  2.08 (0.17), residues: 930
  sheet: -0.92 (0.49), residues: 100
  loop : -0.83 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP B 813 
 HIS   0.006   0.001   HIS B 915 
 PHE   0.012   0.001   PHE A 728 
 TYR   0.014   0.001   TYR A 202 
 ARG   0.002   0.000   ARG B 814 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    4)
  link_NAG-ASN         : angle       1.73843 (   12)
  link_BETA1-4         : bond        0.00672 (    4)
  link_BETA1-4         : angle       3.01876 (   12)
  hydrogen bonds       : bond        0.04352 (  786)
  hydrogen bonds       : angle       4.34768 ( 2262)
  SS BOND              : bond        0.00690 (    6)
  SS BOND              : angle       1.83640 (   12)
  covalent geometry    : bond        0.00306 (13450)
  covalent geometry    : angle       0.63146 (18304)

*********************** 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
  190 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 4.038 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8632 (tpt) cc_final: 0.8403 (tpp)
REVERT: A  280 LEU cc_start: 0.8187 (pp) cc_final: 0.7918 (pp)
REVERT: A  471 LEU cc_start: 0.8741 (mm) cc_final: 0.7532 (tp)
REVERT: A  601 MET cc_start: 0.8115 (tpp) cc_final: 0.7746 (tpp)
REVERT: A  726 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8279 (mm)
REVERT: B  181 MET cc_start: 0.8611 (tpt) cc_final: 0.8353 (tpp)
REVERT: B  263 MET cc_start: 0.7169 (tpp) cc_final: 0.6759 (tpp)
REVERT: B  280 LEU cc_start: 0.8179 (pp) cc_final: 0.7901 (pp)
REVERT: B  597 MET cc_start: 0.8016 (mmm) cc_final: 0.7608 (mmm)
REVERT: B  601 MET cc_start: 0.8130 (tpp) cc_final: 0.7685 (tpp)
REVERT: B  626 ARG cc_start: 0.7421 (ttt-90) cc_final: 0.6685 (tpt170)
REVERT: B  728 PHE cc_start: 0.7620 (t80) cc_final: 0.7326 (t80)
REVERT: B  743 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7591 (p)
REVERT: B 1071 MET cc_start: 0.7663 (tpp) cc_final: 0.7303 (tpp)
REVERT: B 1081 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7113 (mp)
  outliers start: 21
  outliers final: 15
  residues processed: 187
  average time/residue: 0.3293
  time to fit residues: 104.0460
Evaluate side-chains
  179 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
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  276 VAL
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  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 62 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   chunk 137 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 119 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0070
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.7402

-------------------------------------------------------------------------------
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 = 0.4262 r_free = 0.4262 target = 0.157558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.118734 restraints weight = 17835.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.124769 restraints weight = 8674.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.128942 restraints weight = 5487.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13464  Z= 0.127
  Angle     :  0.643  15.884  18340  Z= 0.316
  Chirality :  0.044   0.253   2178
  Planarity :  0.004   0.056   2266
  Dihedral  :  4.652  53.376   1980
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.11 %
    Favored  : 96.77 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.21), residues: 1702
  helix:  2.09 (0.17), residues: 934
  sheet: -0.88 (0.49), residues: 100
  loop : -0.78 (0.24), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 813 
 HIS   0.006   0.001   HIS B 915 
 PHE   0.020   0.001   PHE A 877 
 TYR   0.014   0.001   TYR B 202 
 ARG   0.002   0.000   ARG A 814 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    4)
  link_NAG-ASN         : angle       1.73285 (   12)
  link_BETA1-4         : bond        0.00673 (    4)
  link_BETA1-4         : angle       2.98082 (   12)
  hydrogen bonds       : bond        0.04342 (  786)
  hydrogen bonds       : angle       4.38114 ( 2262)
  SS BOND              : bond        0.00639 (    6)
  SS BOND              : angle       1.76949 (   12)
  covalent geometry    : bond        0.00281 (13450)
  covalent geometry    : angle       0.63548 (18304)

********************** 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
  184 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 1.698 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8612 (tpt) cc_final: 0.8385 (tpp)
REVERT: A  280 LEU cc_start: 0.8188 (pp) cc_final: 0.7922 (pp)
REVERT: A  471 LEU cc_start: 0.8713 (mm) cc_final: 0.7522 (tp)
REVERT: A  597 MET cc_start: 0.7963 (mmm) cc_final: 0.7380 (mmm)
REVERT: A  601 MET cc_start: 0.8071 (tpp) cc_final: 0.7707 (tpp)
REVERT: A  726 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8293 (mm)
REVERT: B  138 MET cc_start: 0.8001 (ppp) cc_final: 0.6711 (ppp)
REVERT: B  181 MET cc_start: 0.8579 (tpt) cc_final: 0.8338 (tpp)
REVERT: B  263 MET cc_start: 0.7158 (tpp) cc_final: 0.6790 (tpp)
REVERT: B  280 LEU cc_start: 0.8185 (pp) cc_final: 0.7911 (pp)
REVERT: B  471 LEU cc_start: 0.8700 (mm) cc_final: 0.7516 (tp)
REVERT: B  597 MET cc_start: 0.7955 (mmm) cc_final: 0.7616 (mmm)
REVERT: B  601 MET cc_start: 0.8088 (tpp) cc_final: 0.7673 (tpp)
REVERT: B  626 ARG cc_start: 0.7366 (ttt-90) cc_final: 0.6683 (tpt170)
REVERT: B  728 PHE cc_start: 0.7631 (t80) cc_final: 0.7351 (t80)
REVERT: B  743 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7562 (p)
REVERT: B 1071 MET cc_start: 0.7692 (tpp) cc_final: 0.7336 (tpp)
REVERT: B 1081 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7102 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 180
  average time/residue: 0.2019
  time to fit residues: 59.8527
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  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
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  276 VAL
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  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 40 optimal weight:    0.8980
   chunk 147 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   chunk 144 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4247 r_free = 0.4247 target = 0.156165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.117358 restraints weight = 18073.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.123301 restraints weight = 8829.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.127463 restraints weight = 5611.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13464  Z= 0.128
  Angle     :  0.634  11.753  18340  Z= 0.313
  Chirality :  0.044   0.253   2178
  Planarity :  0.004   0.054   2266
  Dihedral  :  4.654  53.677   1980
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.23 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 19.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.21), residues: 1702
  helix:  2.03 (0.17), residues: 944
  sheet: -0.83 (0.49), residues: 100
  loop : -0.76 (0.25), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP B 813 
 HIS   0.006   0.001   HIS B 915 
 PHE   0.010   0.001   PHE B 728 
 TYR   0.014   0.001   TYR B 202 
 ARG   0.001   0.000   ARG B 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00180 (    4)
  link_NAG-ASN         : angle       1.66134 (   12)
  link_BETA1-4         : bond        0.00674 (    4)
  link_BETA1-4         : angle       2.93603 (   12)
  hydrogen bonds       : bond        0.04263 (  786)
  hydrogen bonds       : angle       4.39690 ( 2262)
  SS BOND              : bond        0.00634 (    6)
  SS BOND              : angle       1.70094 (   12)
  covalent geometry    : bond        0.00285 (13450)
  covalent geometry    : angle       0.62706 (18304)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5238.73 seconds
wall clock time: 94 minutes 9.71 seconds (5649.71 seconds total)