Starting phenix.real_space_refine
on Tue Mar  3 21:15:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kku_0703/03_2026/6kku_0703.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kku_0703/03_2026/6kku_0703.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kku_0703/03_2026/6kku_0703.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kku_0703/03_2026/6kku_0703.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kku_0703/03_2026/6kku_0703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kku_0703/03_2026/6kku_0703.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     Cl      2      4.86       5
     C    5544      2.51       5
     N    1284      2.21       5
     O    1514      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8412
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 4068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4068
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 26, 'TRANS': 510}
    Chain: "B"
      Number of atoms: 4068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4068
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 26, 'TRANS': 510}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "J"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {' CL': 1, 'DU0': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {' CL': 1, 'DU0': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.41, per 1000 atoms: 0.29
  Number of scatterers: 8412
  At special positions: 0
  Unit cell: (78.11, 101.65, 102.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      68     16.00
     O    1514      8.00
     N    1284      7.00
     C    5544      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 163 " - pdb=" SG  CYS A 626 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 353 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 163 " - pdb=" SG  CYS B 626 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 308 " - pdb=" SG  CYS B 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 343 " - pdb=" SG  CYS B 353 " 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=4, symmetry=0
  Links applied
    ALPHA1-4
      " BGC E   1 " - " GLC E   2 "
      " BGC F   1 " - " GLC F   2 "
      " BGC I   1 " - " GLC I   2 "
      " BGC J   1 " - " GLC J   2 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 312 "
      " NAG D   1 " - " ASN A 361 "
      " NAG G   1 " - " ASN B 312 "
      " NAG H   1 " - " ASN B 361 "
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 341.5 milliseconds
  

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      69.3% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 124 through 133
      removed outlier: 3.916A  pdb=" N   PHE A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 140
    Processing helix  chain 'A' and resid 141 through 176
      removed outlier: 7.212A  pdb=" N   VAL A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 8.871A  pdb=" N   LEU A 151 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   CYS A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   THR A 164 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 166 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 193
      removed outlier: 3.977A  pdb=" N   ILE A 189 " --> pdb=" O   SER A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 227
      removed outlier: 3.522A  pdb=" N   GLY A 198 " --> pdb=" O   GLY A 194 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA A 214 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 269
      removed outlier: 3.589A  pdb=" N   VAL A 253 " --> pdb=" O   ASN A 249 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TYR A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU A 264 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A 266 " --> pdb=" O   MET A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 276
    Processing helix  chain 'A' and resid 278 through 298
    Processing helix  chain 'A' and resid 336 through 344
      removed outlier: 3.526A  pdb=" N   PHE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 3.567A  pdb=" N   ASN A 360 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 379
      removed outlier: 3.565A  pdb=" N   LEU A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 3.908A  pdb=" N   SER A 407 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 428
      removed outlier: 3.650A  pdb=" N   LEU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 434 through 438
    Processing helix  chain 'A' and resid 446 through 477
      removed outlier: 3.633A  pdb=" N   ILE A 451 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
      Proline residue:  A 452  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE A 456 " --> pdb=" O   PRO A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 4.178A  pdb=" N   ASP A 488 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 500
    Processing helix  chain 'A' and resid 504 through 536
      Proline residue:  A 527  - end of helix
      removed outlier: 3.540A  pdb=" N   ASP A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
      removed outlier: 5.406A  pdb=" N   VAL A 544 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   HIS A 547 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 570
      removed outlier: 3.895A  pdb=" N   LEU A 559 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A 567 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 602
      Proline residue:  A 579  - end of helix
      removed outlier: 3.751A  pdb=" N   GLN A 599 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   THR A 600 " --> pdb=" O   CYS A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 634
      removed outlier: 3.741A  pdb=" N   SER A 619 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER A 634 " --> pdb=" O   MET A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 652
      removed outlier: 3.508A  pdb=" N   ALA A 638 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 133
      removed outlier: 3.916A  pdb=" N   PHE B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 140
    Processing helix  chain 'B' and resid 141 through 176
      removed outlier: 7.212A  pdb=" N   VAL B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 8.871A  pdb=" N   LEU B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN B 152 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   CYS B 162 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   CYS B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   THR B 164 " --> pdb=" O   CYS B 160 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B 166 " --> pdb=" O   CYS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 193
      removed outlier: 3.976A  pdb=" N   ILE B 189 " --> pdb=" O   SER B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 227
      removed outlier: 3.522A  pdb=" N   GLY B 198 " --> pdb=" O   GLY B 194 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 214 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 269
      removed outlier: 3.589A  pdb=" N   VAL B 253 " --> pdb=" O   ASN B 249 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TYR B 254 " --> pdb=" O   ASN B 250 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU B 264 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL B 266 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 276
    Processing helix  chain 'B' and resid 278 through 298
    Processing helix  chain 'B' and resid 336 through 344
      removed outlier: 3.526A  pdb=" N   PHE B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 3.566A  pdb=" N   ASN B 360 " --> pdb=" O   TYR B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 379
      removed outlier: 3.566A  pdb=" N   LEU B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.908A  pdb=" N   SER B 407 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 428
      removed outlier: 3.649A  pdb=" N   LEU B 423 " --> pdb=" O   SER B 419 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY B 425 " --> pdb=" O   THR B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 431
      No H-bonds generated for 'chain 'B' and resid 429 through 431'
    Processing helix  chain 'B' and resid 434 through 438
    Processing helix  chain 'B' and resid 446 through 477
      removed outlier: 3.632A  pdb=" N   ILE B 451 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
      Proline residue:  B 452  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE B 456 " --> pdb=" O   PRO B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 483
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 4.179A  pdb=" N   ASP B 488 " --> pdb=" O   LYS B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 500
    Processing helix  chain 'B' and resid 504 through 536
      Proline residue:  B 527  - end of helix
      removed outlier: 3.539A  pdb=" N   ASP B 536 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 547
      removed outlier: 5.405A  pdb=" N   VAL B 544 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS B 547 " --> pdb=" O   VAL B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 570
      removed outlier: 3.895A  pdb=" N   LEU B 559 " --> pdb=" O   THR B 555 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 567 " --> pdb=" O   LEU B 563 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 602
      Proline residue:  B 579  - end of helix
      removed outlier: 3.751A  pdb=" N   GLN B 599 " --> pdb=" O   ALA B 595 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   THR B 600 " --> pdb=" O   CYS B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 615 through 634
      removed outlier: 3.740A  pdb=" N   SER B 619 " --> pdb=" O   HIS B 615 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER B 634 " --> pdb=" O   MET B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 652
      removed outlier: 3.508A  pdb=" N   ALA B 638 " --> pdb=" O   SER B 634 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329
    Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 329

    486 hydrogen bonds defined for protein.
    1386 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2474
        1.35 -     1.47: 2313
        1.47 -     1.60: 3735
        1.60 -     1.72: 0
        1.72 -     1.85: 104
  Bond restraints: 8626
  Sorted by residual:
  bond pdb=" C5  GLC F   2 "
       pdb=" O5  GLC F   2 "
    ideal  model  delta    sigma   weight residual
    1.415  1.503 -0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" C5  GLC I   2 "
       pdb=" O5  GLC I   2 "
    ideal  model  delta    sigma   weight residual
    1.415  1.503 -0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" C1  BGC E   1 "
       pdb=" O5  BGC E   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.494 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C1  BGC J   1 "
       pdb=" O5  BGC J   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.494 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C1  GLC I   2 "
       pdb=" O5  GLC I   2 "
    ideal  model  delta    sigma   weight residual
    1.402  1.485 -0.083 2.00e-02 2.50e+03 1.71e+01
  ... (remaining 8621 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 11066
        1.95 -     3.89: 558
        3.89 -     5.84: 122
        5.84 -     7.79: 35
        7.79 -     9.73: 13
  Bond angle restraints: 11794
  Sorted by residual:
  angle pdb=" CA  PRO A 230 "
        pdb=" C   PRO A 230 "
        pdb=" N   PRO A 231 "
      ideal   model   delta    sigma   weight residual
     117.93  122.96   -5.03 1.20e+00 6.94e-01 1.75e+01
  angle pdb=" CA  PRO B 230 "
        pdb=" C   PRO B 230 "
        pdb=" N   PRO B 231 "
      ideal   model   delta    sigma   weight residual
     117.93  122.90   -4.97 1.20e+00 6.94e-01 1.72e+01
  angle pdb=" N   VAL A 490 "
        pdb=" CA  VAL A 490 "
        pdb=" C   VAL A 490 "
      ideal   model   delta    sigma   weight residual
     106.53  111.67   -5.14 1.41e+00 5.03e-01 1.33e+01
  angle pdb=" N   PHE A 428 "
        pdb=" CA  PHE A 428 "
        pdb=" C   PHE A 428 "
      ideal   model   delta    sigma   weight residual
     113.16  118.28   -5.12 1.42e+00 4.96e-01 1.30e+01
  angle pdb=" N   PHE B 428 "
        pdb=" CA  PHE B 428 "
        pdb=" C   PHE B 428 "
      ideal   model   delta    sigma   weight residual
     113.16  118.28   -5.12 1.42e+00 4.96e-01 1.30e+01
  ... (remaining 11789 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.22: 5236
       34.22 -    68.43: 54
       68.43 -   102.65: 42
      102.65 -   136.86: 32
      136.86 -   171.08: 2
  Dihedral angle restraints: 5366
    sinusoidal: 2284
      harmonic: 3082
  Sorted by residual:
  dihedral pdb=" C26 DU0 A1106 "
           pdb=" C24 DU0 A1106 "
           pdb=" C25 DU0 A1106 "
           pdb=" O23 DU0 A1106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     189.32   18.24  171.08     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C26 DU0 B1108 "
           pdb=" C24 DU0 B1108 "
           pdb=" C25 DU0 B1108 "
           pdb=" O23 DU0 B1108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     189.32   18.24  171.08     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" O2  GLC F   2 "
           pdb=" C2  GLC F   2 "
           pdb=" C3  GLC F   2 "
           pdb=" O3  GLC F   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.18 -167.16 -132.66     1      3.00e+01 1.11e-03 1.79e+01
  ... (remaining 5363 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1212
       0.080 -    0.160: 237
       0.160 -    0.240: 15
       0.240 -    0.319: 0
       0.319 -    0.399: 2
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN B 312 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.80    0.40 2.00e-01 2.50e+01 3.98e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 312 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.80    0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" C1  GLC F   2 "
            pdb=" O4  BGC F   1 "
            pdb=" C2  GLC F   2 "
            pdb=" O5  GLC F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.37    0.03 2.00e-02 2.50e+03 1.68e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 408 "   -0.048 5.00e-02 4.00e+02   7.13e-02 8.13e+00
        pdb=" N   PRO B 409 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 409 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 409 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 408 "   -0.048 5.00e-02 4.00e+02   7.13e-02 8.12e+00
        pdb=" N   PRO A 409 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 409 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 409 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 467 "   -0.016 2.00e-02 2.50e+03   1.66e-02 4.81e+00
        pdb=" CG  PHE A 467 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 467 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 467 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 467 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 467 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 467 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1405 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1782
        2.77 -     3.31: 7841
        3.31 -     3.84: 13265
        3.84 -     4.37: 14998
        4.37 -     4.90: 26580
  Nonbonded interactions: 64466
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 292 "
            pdb=" OG  SER A 468 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OH  TYR B 292 "
            pdb=" OG  SER B 468 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   ILE A 169 "
            pdb=" OG  SER A 172 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   ILE B 169 "
            pdb=" OG  SER B 172 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O2  GLC F   2 "
            pdb=" O4  GLC F   2 "
     model   vdw
     2.383 3.040
  ... (remaining 64461 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.800
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
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      :  0.009   0.088   8648  Z= 0.409
  Angle     :  1.170  14.844  11842  Z= 0.560
  Chirality :  0.061   0.399   1466
  Planarity :  0.008   0.071   1404
  Dihedral  : 18.283 171.079   3380
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.36 (0.21), residues: 1070
  helix: -1.68 (0.16), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.97 (0.25), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 445 
 TYR   0.025   0.003   TYR A 292 
 PHE   0.039   0.004   PHE A 467 
 TRP   0.031   0.003   TRP A 339 
 HIS   0.006   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00915 ( 8626)
  covalent geometry    : angle       1.08193 (11794)
  SS BOND              : bond        0.00252 (    6)
  SS BOND              : angle       2.54088 (   12)
  hydrogen bonds       : bond        0.16407 (  486)
  hydrogen bonds       : angle       6.16497 ( 1386)
  Misc. bond           : bond        0.00749 (    4)
  link_ALPHA1-4        : bond        0.05558 (    4)
  link_ALPHA1-4        : angle       2.30409 (   12)
  link_BETA1-4         : bond        0.02270 (    4)
  link_BETA1-4         : angle      10.74578 (   12)
  link_NAG-ASN         : bond        0.00864 (    4)
  link_NAG-ASN         : angle       8.61615 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  180 VAL cc_start: 0.8404 (t) cc_final: 0.8171 (t)
REVERT: A  297 LYS cc_start: 0.8587 (tttm) cc_final: 0.7946 (mmtm)
REVERT: A  405 LYS cc_start: 0.8370 (tttp) cc_final: 0.7860 (ttpp)
REVERT: B  144 MET cc_start: 0.8255 (ttm) cc_final: 0.7999 (ttt)
REVERT: B  176 THR cc_start: 0.8818 (p) cc_final: 0.8436 (t)
REVERT: B  297 LYS cc_start: 0.8699 (tttm) cc_final: 0.7868 (mmtm)
REVERT: B  405 LYS cc_start: 0.8357 (tttp) cc_final: 0.7862 (ttpp)
REVERT: B  484 ASP cc_start: 0.8380 (m-30) cc_final: 0.8071 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.0980
  time to fit residues: 38.4807
Evaluate side-chains
  139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN
A 531 GLN
B 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.132592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108717 restraints weight = 13873.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.112022 restraints weight = 7844.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.114119 restraints weight = 5536.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115307 restraints weight = 4470.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.116181 restraints weight = 3938.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8648  Z= 0.157
  Angle     :  0.760  10.051  11842  Z= 0.348
  Chirality :  0.044   0.228   1466
  Planarity :  0.005   0.068   1404
  Dihedral  : 15.335 151.036   1648
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.43 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.24), residues: 1070
  helix:  0.61 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.62 (0.26), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 445 
 TYR   0.017   0.001   TYR A 613 
 PHE   0.013   0.002   PHE B 428 
 TRP   0.016   0.001   TRP A 616 
 HIS   0.003   0.001   HIS A 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8626)
  covalent geometry    : angle       0.71244 (11794)
  SS BOND              : bond        0.00139 (    6)
  SS BOND              : angle       1.37171 (   12)
  hydrogen bonds       : bond        0.04843 (  486)
  hydrogen bonds       : angle       4.08298 ( 1386)
  Misc. bond           : bond        0.00085 (    4)
  link_ALPHA1-4        : bond        0.00852 (    4)
  link_ALPHA1-4        : angle       2.11968 (   12)
  link_BETA1-4         : bond        0.01033 (    4)
  link_BETA1-4         : angle       6.57784 (   12)
  link_NAG-ASN         : bond        0.00057 (    4)
  link_NAG-ASN         : angle       4.61734 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  537 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8232 (t0)
REVERT: B  130 GLN cc_start: 0.8067 (tt0) cc_final: 0.7722 (tt0)
REVERT: B  144 MET cc_start: 0.8063 (ttm) cc_final: 0.7738 (ttt)
REVERT: B  380 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8491 (mt)
REVERT: B  490 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8035 (p)
REVERT: B  537 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8026 (t0)
  outliers start: 21
  outliers final: 6
  residues processed: 181
  average time/residue: 0.0733
  time to fit residues: 19.4827
Evaluate side-chains
  144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 ASN
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.134484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.110439 restraints weight = 13625.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.113766 restraints weight = 7743.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.115928 restraints weight = 5466.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.117245 restraints weight = 4399.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.118110 restraints weight = 3847.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8648  Z= 0.128
  Angle     :  0.695   9.642  11842  Z= 0.324
  Chirality :  0.044   0.274   1466
  Planarity :  0.004   0.053   1404
  Dihedral  : 12.705 149.263   1648
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.79 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.25), residues: 1070
  helix:  1.37 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.23 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 445 
 TYR   0.016   0.001   TYR B 613 
 PHE   0.027   0.001   PHE B 261 
 TRP   0.017   0.001   TRP B 616 
 HIS   0.005   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8626)
  covalent geometry    : angle       0.64595 (11794)
  SS BOND              : bond        0.00390 (    6)
  SS BOND              : angle       2.30099 (   12)
  hydrogen bonds       : bond        0.04371 (  486)
  hydrogen bonds       : angle       3.97555 ( 1386)
  Misc. bond           : bond        0.00029 (    4)
  link_ALPHA1-4        : bond        0.00988 (    4)
  link_ALPHA1-4        : angle       1.52492 (   12)
  link_BETA1-4         : bond        0.01228 (    4)
  link_BETA1-4         : angle       6.38949 (   12)
  link_NAG-ASN         : bond        0.00174 (    4)
  link_NAG-ASN         : angle       4.29038 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 LYS cc_start: 0.8003 (tttp) cc_final: 0.7614 (ttpp)
REVERT: A  416 ILE cc_start: 0.8427 (pt) cc_final: 0.8213 (pt)
REVERT: B  130 GLN cc_start: 0.8025 (tt0) cc_final: 0.7693 (tt0)
REVERT: B  144 MET cc_start: 0.8037 (ttm) cc_final: 0.7793 (ttt)
REVERT: B  251 MET cc_start: 0.8676 (mmm) cc_final: 0.8459 (mtp)
REVERT: B  380 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8265 (mt)
REVERT: B  405 LYS cc_start: 0.7904 (tttp) cc_final: 0.7555 (ttpp)
REVERT: B  410 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8308 (tt)
REVERT: B  537 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8118 (t0)
  outliers start: 22
  outliers final: 9
  residues processed: 174
  average time/residue: 0.0755
  time to fit residues: 19.2175
Evaluate side-chains
  151 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:    0.1980
   chunk 84 optimal weight:    0.3980
   chunk 8 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0370
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 493 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.136251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.111687 restraints weight = 13825.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.115045 restraints weight = 7804.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.117246 restraints weight = 5508.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118620 restraints weight = 4438.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119522 restraints weight = 3878.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8648  Z= 0.120
  Angle     :  0.671   8.725  11842  Z= 0.308
  Chirality :  0.042   0.245   1466
  Planarity :  0.004   0.044   1404
  Dihedral  : 11.061 143.778   1648
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.59 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1070
  helix:  1.93 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.14 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 445 
 TYR   0.016   0.001   TYR B 613 
 PHE   0.010   0.001   PHE A 467 
 TRP   0.018   0.001   TRP B 616 
 HIS   0.002   0.000   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8626)
  covalent geometry    : angle       0.62567 (11794)
  SS BOND              : bond        0.00405 (    6)
  SS BOND              : angle       1.86471 (   12)
  hydrogen bonds       : bond        0.03819 (  486)
  hydrogen bonds       : angle       3.74255 ( 1386)
  Misc. bond           : bond        0.00017 (    4)
  link_ALPHA1-4        : bond        0.01348 (    4)
  link_ALPHA1-4        : angle       2.01678 (   12)
  link_BETA1-4         : bond        0.01172 (    4)
  link_BETA1-4         : angle       5.97603 (   12)
  link_NAG-ASN         : bond        0.00239 (    4)
  link_NAG-ASN         : angle       3.96458 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.7937 (tt0) cc_final: 0.7727 (tt0)
REVERT: A  380 LEU cc_start: 0.8591 (mt) cc_final: 0.8329 (mt)
REVERT: A  405 LYS cc_start: 0.7949 (tttp) cc_final: 0.7586 (ttpp)
REVERT: A  594 LEU cc_start: 0.9135 (tp) cc_final: 0.8838 (tp)
REVERT: B  130 GLN cc_start: 0.7997 (tt0) cc_final: 0.7693 (tt0)
REVERT: B  251 MET cc_start: 0.8597 (mmm) cc_final: 0.8341 (mtp)
REVERT: B  380 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: B  405 LYS cc_start: 0.7856 (tttp) cc_final: 0.7526 (ttpp)
REVERT: B  410 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8382 (tt)
  outliers start: 23
  outliers final: 13
  residues processed: 171
  average time/residue: 0.0782
  time to fit residues: 19.4766
Evaluate side-chains
  154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  521 GLN
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  600 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:    0.0270
   chunk 87 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0670
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0060
   overall best weight:    0.3392

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.137601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.113201 restraints weight = 13679.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116571 restraints weight = 7792.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.118777 restraints weight = 5521.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.120030 restraints weight = 4452.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120989 restraints weight = 3915.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8648  Z= 0.116
  Angle     :  0.656   8.406  11842  Z= 0.299
  Chirality :  0.042   0.229   1466
  Planarity :  0.004   0.040   1404
  Dihedral  :  9.879 138.050   1648
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.51 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.26), residues: 1070
  helix:  2.22 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.04 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 445 
 TYR   0.014   0.001   TYR B 613 
 PHE   0.021   0.001   PHE B 261 
 TRP   0.012   0.001   TRP A 616 
 HIS   0.002   0.000   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8626)
  covalent geometry    : angle       0.61475 (11794)
  SS BOND              : bond        0.00368 (    6)
  SS BOND              : angle       1.46219 (   12)
  hydrogen bonds       : bond        0.03503 (  486)
  hydrogen bonds       : angle       3.62433 ( 1386)
  Misc. bond           : bond        0.00015 (    4)
  link_ALPHA1-4        : bond        0.01429 (    4)
  link_ALPHA1-4        : angle       1.83279 (   12)
  link_BETA1-4         : bond        0.01243 (    4)
  link_BETA1-4         : angle       5.76411 (   12)
  link_NAG-ASN         : bond        0.00260 (    4)
  link_NAG-ASN         : angle       3.77907 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.7942 (tt0) cc_final: 0.7694 (tt0)
REVERT: A  144 MET cc_start: 0.8109 (ttm) cc_final: 0.7792 (ttt)
REVERT: A  380 LEU cc_start: 0.8586 (mt) cc_final: 0.8363 (mt)
REVERT: A  405 LYS cc_start: 0.7889 (tttp) cc_final: 0.7542 (ttpp)
REVERT: A  594 LEU cc_start: 0.9059 (tp) cc_final: 0.8784 (tp)
REVERT: B  130 GLN cc_start: 0.7952 (tt0) cc_final: 0.7748 (tt0)
REVERT: B  251 MET cc_start: 0.8526 (mmm) cc_final: 0.8313 (mtp)
REVERT: B  297 LYS cc_start: 0.8697 (tttm) cc_final: 0.7751 (mmtt)
REVERT: B  380 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8314 (mt)
REVERT: B  405 LYS cc_start: 0.7806 (tttp) cc_final: 0.7489 (ttpp)
REVERT: B  410 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8456 (tt)
REVERT: B  594 LEU cc_start: 0.9028 (tp) cc_final: 0.8750 (tp)
REVERT: B  647 MET cc_start: 0.8410 (ttp) cc_final: 0.8179 (ttp)
  outliers start: 23
  outliers final: 10
  residues processed: 173
  average time/residue: 0.0794
  time to fit residues: 20.1284
Evaluate side-chains
  153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  547 HIS
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  600 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.136592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.112216 restraints weight = 13698.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.115529 restraints weight = 7804.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117697 restraints weight = 5544.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.119064 restraints weight = 4489.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.119872 restraints weight = 3921.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8648  Z= 0.122
  Angle     :  0.675   9.059  11842  Z= 0.307
  Chirality :  0.042   0.223   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  9.019 135.531   1648
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.85 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.26), residues: 1070
  helix:  2.32 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.97 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 445 
 TYR   0.016   0.001   TYR A 613 
 PHE   0.012   0.001   PHE A 428 
 TRP   0.014   0.001   TRP B 616 
 HIS   0.003   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8626)
  covalent geometry    : angle       0.63505 (11794)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       1.47746 (   12)
  hydrogen bonds       : bond        0.03557 (  486)
  hydrogen bonds       : angle       3.60552 ( 1386)
  Misc. bond           : bond        0.00020 (    4)
  link_ALPHA1-4        : bond        0.01428 (    4)
  link_ALPHA1-4        : angle       1.97519 (   12)
  link_BETA1-4         : bond        0.01197 (    4)
  link_BETA1-4         : angle       5.67810 (   12)
  link_NAG-ASN         : bond        0.00171 (    4)
  link_NAG-ASN         : angle       3.85893 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.7930 (tt0) cc_final: 0.7723 (tt0)
REVERT: A  144 MET cc_start: 0.8144 (ttm) cc_final: 0.7816 (ttt)
REVERT: A  380 LEU cc_start: 0.8616 (mt) cc_final: 0.8376 (mt)
REVERT: A  405 LYS cc_start: 0.7921 (tttp) cc_final: 0.7556 (ttpp)
REVERT: A  594 LEU cc_start: 0.9052 (tp) cc_final: 0.8815 (tp)
REVERT: B  130 GLN cc_start: 0.8016 (tt0) cc_final: 0.7760 (tt0)
REVERT: B  262 MET cc_start: 0.8164 (mtm) cc_final: 0.7927 (mtt)
REVERT: B  380 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8342 (mt)
REVERT: B  405 LYS cc_start: 0.7866 (tttp) cc_final: 0.7523 (ttpp)
REVERT: B  594 LEU cc_start: 0.9037 (tp) cc_final: 0.8797 (tt)
REVERT: B  647 MET cc_start: 0.8459 (ttp) cc_final: 0.8245 (ttp)
  outliers start: 17
  outliers final: 12
  residues processed: 156
  average time/residue: 0.0794
  time to fit residues: 18.0465
Evaluate side-chains
  150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  600 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    0.0070
   chunk 104 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.137281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.112824 restraints weight = 13815.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.116186 restraints weight = 7847.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.118358 restraints weight = 5574.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119652 restraints weight = 4512.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120521 restraints weight = 3963.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8648  Z= 0.118
  Angle     :  0.666   8.414  11842  Z= 0.304
  Chirality :  0.042   0.213   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  7.984 134.180   1648
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.10 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.26), residues: 1070
  helix:  2.39 (0.21), residues: 636
  sheet:  1.26 (1.11), residues: 20
  loop : -1.95 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 445 
 TYR   0.016   0.001   TYR B 613 
 PHE   0.011   0.001   PHE B 235 
 TRP   0.012   0.001   TRP B 616 
 HIS   0.002   0.000   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8626)
  covalent geometry    : angle       0.62664 (11794)
  SS BOND              : bond        0.00341 (    6)
  SS BOND              : angle       1.37624 (   12)
  hydrogen bonds       : bond        0.03483 (  486)
  hydrogen bonds       : angle       3.60506 ( 1386)
  Misc. bond           : bond        0.00030 (    4)
  link_ALPHA1-4        : bond        0.01594 (    4)
  link_ALPHA1-4        : angle       1.93683 (   12)
  link_BETA1-4         : bond        0.01222 (    4)
  link_BETA1-4         : angle       5.61819 (   12)
  link_NAG-ASN         : bond        0.00234 (    4)
  link_NAG-ASN         : angle       3.76591 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8182 (ttm) cc_final: 0.7874 (ttt)
REVERT: A  380 LEU cc_start: 0.8684 (mt) cc_final: 0.8417 (mt)
REVERT: A  405 LYS cc_start: 0.7851 (tttp) cc_final: 0.7506 (ttpp)
REVERT: A  594 LEU cc_start: 0.9041 (tp) cc_final: 0.8805 (tt)
REVERT: B  130 GLN cc_start: 0.8003 (tt0) cc_final: 0.7789 (tt0)
REVERT: B  380 LEU cc_start: 0.8691 (mt) cc_final: 0.8322 (mt)
REVERT: B  405 LYS cc_start: 0.7818 (tttp) cc_final: 0.7489 (ttpp)
REVERT: B  594 LEU cc_start: 0.9057 (tp) cc_final: 0.8827 (tt)
  outliers start: 13
  outliers final: 10
  residues processed: 159
  average time/residue: 0.0795
  time to fit residues: 18.3695
Evaluate side-chains
  150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 86 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0980
   chunk 100 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.135334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.110904 restraints weight = 13801.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.114158 restraints weight = 7844.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.116284 restraints weight = 5590.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.117471 restraints weight = 4530.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.118404 restraints weight = 4006.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8648  Z= 0.140
  Angle     :  0.691   8.296  11842  Z= 0.319
  Chirality :  0.043   0.219   1466
  Planarity :  0.004   0.040   1404
  Dihedral  :  7.401 134.717   1648
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.76 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.26), residues: 1070
  helix:  2.32 (0.21), residues: 648
  sheet:  1.44 (1.12), residues: 20
  loop : -2.01 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 317 
 TYR   0.016   0.001   TYR B 613 
 PHE   0.013   0.001   PHE B 428 
 TRP   0.009   0.001   TRP A 339 
 HIS   0.004   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8626)
  covalent geometry    : angle       0.65152 (11794)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       1.52240 (   12)
  hydrogen bonds       : bond        0.03776 (  486)
  hydrogen bonds       : angle       3.67523 ( 1386)
  Misc. bond           : bond        0.00033 (    4)
  link_ALPHA1-4        : bond        0.01616 (    4)
  link_ALPHA1-4        : angle       1.97903 (   12)
  link_BETA1-4         : bond        0.01150 (    4)
  link_BETA1-4         : angle       5.66050 (   12)
  link_NAG-ASN         : bond        0.00067 (    4)
  link_NAG-ASN         : angle       4.01720 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.8743 (mt) cc_final: 0.8475 (mt)
REVERT: A  594 LEU cc_start: 0.9047 (tp) cc_final: 0.8822 (tt)
REVERT: B  380 LEU cc_start: 0.8745 (mt) cc_final: 0.8369 (mt)
REVERT: B  405 LYS cc_start: 0.7884 (tttp) cc_final: 0.7546 (ttpp)
REVERT: B  594 LEU cc_start: 0.9045 (tp) cc_final: 0.8825 (tt)
  outliers start: 20
  outliers final: 16
  residues processed: 153
  average time/residue: 0.0718
  time to fit residues: 16.1088
Evaluate side-chains
  153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 42 optimal weight:    0.0060
   chunk 64 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 105 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0370
   chunk 26 optimal weight:    0.3980
   chunk 41 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.4674

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.113286 restraints weight = 13663.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.116599 restraints weight = 7806.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.118769 restraints weight = 5574.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120150 restraints weight = 4510.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.120856 restraints weight = 3943.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8648  Z= 0.118
  Angle     :  0.677   9.750  11842  Z= 0.311
  Chirality :  0.042   0.203   1466
  Planarity :  0.004   0.037   1404
  Dihedral  :  7.124 134.679   1648
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.99 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.26), residues: 1070
  helix:  2.38 (0.21), residues: 648
  sheet:  1.47 (1.12), residues: 20
  loop : -1.89 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 317 
 TYR   0.015   0.001   TYR B 613 
 PHE   0.012   0.001   PHE A 541 
 TRP   0.011   0.001   TRP B 616 
 HIS   0.002   0.000   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8626)
  covalent geometry    : angle       0.63993 (11794)
  SS BOND              : bond        0.00305 (    6)
  SS BOND              : angle       1.34146 (   12)
  hydrogen bonds       : bond        0.03494 (  486)
  hydrogen bonds       : angle       3.65214 ( 1386)
  Misc. bond           : bond        0.00035 (    4)
  link_ALPHA1-4        : bond        0.01465 (    4)
  link_ALPHA1-4        : angle       1.71850 (   12)
  link_BETA1-4         : bond        0.01192 (    4)
  link_BETA1-4         : angle       5.58409 (   12)
  link_NAG-ASN         : bond        0.00259 (    4)
  link_NAG-ASN         : angle       3.69383 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8068 (ttm) cc_final: 0.7783 (ttt)
REVERT: A  380 LEU cc_start: 0.8729 (mt) cc_final: 0.8424 (mt)
REVERT: A  405 LYS cc_start: 0.7801 (tttp) cc_final: 0.7454 (ttpp)
REVERT: A  594 LEU cc_start: 0.9049 (tp) cc_final: 0.8844 (tt)
REVERT: B  380 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8315 (mt)
REVERT: B  405 LYS cc_start: 0.7777 (tttp) cc_final: 0.7461 (ttpp)
REVERT: B  594 LEU cc_start: 0.9036 (tp) cc_final: 0.8833 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 156
  average time/residue: 0.0777
  time to fit residues: 17.6136
Evaluate side-chains
  157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   chunk 92 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 130 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.137269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.112886 restraints weight = 13673.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.116168 restraints weight = 7783.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.118289 restraints weight = 5561.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119490 restraints weight = 4513.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.120477 restraints weight = 3988.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8648  Z= 0.122
  Angle     :  0.681   9.523  11842  Z= 0.314
  Chirality :  0.043   0.210   1466
  Planarity :  0.004   0.037   1404
  Dihedral  :  7.022 134.059   1648
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.33 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.27), residues: 1070
  helix:  2.37 (0.21), residues: 650
  sheet:  1.38 (1.13), residues: 20
  loop : -1.85 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 191 
 TYR   0.015   0.001   TYR B 613 
 PHE   0.010   0.001   PHE B 428 
 TRP   0.009   0.001   TRP B 616 
 HIS   0.003   0.000   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8626)
  covalent geometry    : angle       0.64395 (11794)
  SS BOND              : bond        0.00359 (    6)
  SS BOND              : angle       1.38912 (   12)
  hydrogen bonds       : bond        0.03490 (  486)
  hydrogen bonds       : angle       3.65453 ( 1386)
  Misc. bond           : bond        0.00032 (    4)
  link_ALPHA1-4        : bond        0.01428 (    4)
  link_ALPHA1-4        : angle       1.78986 (   12)
  link_BETA1-4         : bond        0.01181 (    4)
  link_BETA1-4         : angle       5.55455 (   12)
  link_NAG-ASN         : bond        0.00200 (    4)
  link_NAG-ASN         : angle       3.77883 (   12)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8085 (ttm) cc_final: 0.7789 (ttt)
REVERT: A  380 LEU cc_start: 0.8751 (mt) cc_final: 0.8436 (mt)
REVERT: A  405 LYS cc_start: 0.7818 (tttp) cc_final: 0.7460 (ttpp)
REVERT: A  528 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7535 (mmt-90)
REVERT: A  594 LEU cc_start: 0.9039 (tp) cc_final: 0.8822 (tt)
REVERT: B  380 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8326 (mt)
REVERT: B  405 LYS cc_start: 0.7798 (tttp) cc_final: 0.7470 (ttpp)
  outliers start: 13
  outliers final: 11
  residues processed: 150
  average time/residue: 0.0876
  time to fit residues: 18.5410
Evaluate side-chains
  152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  130 GLN
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 86 optimal weight:    0.0000
   chunk 21 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 521 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.134708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.110415 restraints weight = 13673.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.113658 restraints weight = 7857.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.115723 restraints weight = 5622.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.116883 restraints weight = 4579.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117804 restraints weight = 4056.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8648  Z= 0.154
  Angle     :  0.709   9.181  11842  Z= 0.327
  Chirality :  0.044   0.229   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  7.004 135.046   1648
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 16.33 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.27), residues: 1070
  helix:  2.33 (0.21), residues: 648
  sheet:  1.35 (1.14), residues: 20
  loop : -1.85 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 440 
 TYR   0.015   0.001   TYR B 613 
 PHE   0.013   0.001   PHE B 428 
 TRP   0.010   0.001   TRP A 339 
 HIS   0.003   0.001   HIS B 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8626)
  covalent geometry    : angle       0.67115 (11794)
  SS BOND              : bond        0.00460 (    6)
  SS BOND              : angle       1.56911 (   12)
  hydrogen bonds       : bond        0.03766 (  486)
  hydrogen bonds       : angle       3.74714 ( 1386)
  Misc. bond           : bond        0.00020 (    4)
  link_ALPHA1-4        : bond        0.01341 (    4)
  link_ALPHA1-4        : angle       1.80245 (   12)
  link_BETA1-4         : bond        0.01159 (    4)
  link_BETA1-4         : angle       5.63065 (   12)
  link_NAG-ASN         : bond        0.00036 (    4)
  link_NAG-ASN         : angle       4.01136 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1378.29 seconds
wall clock time: 24 minutes 31.25 seconds (1471.25 seconds total)