Starting phenix.real_space_refine
on Sat Aug 23 00:39:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i3b_35148/08_2025/8i3b_35148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3b_35148/08_2025/8i3b_35148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3b_35148/08_2025/8i3b_35148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3b_35148/08_2025/8i3b_35148.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3b_35148/08_2025/8i3b_35148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3b_35148/08_2025/8i3b_35148.map"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.052
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
     P       6      5.49       5
     S      52      5.16       5
     C    5624      2.51       5
     N    1446      2.21       5
     O    1518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8646
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4292
          Classifications: {'peptide': 550}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 530}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 4292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4292
          Classifications: {'peptide': 550}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 530}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.42, per 1000 atoms: 0.28
  Number of scatterers: 8646
  At special positions: 0
  Unit cell: (80.51, 93.79, 122.01, 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)
     S      52     16.00
     P       6     15.00
     O    1518      8.00
     N    1446      7.00
     C    5624      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 332.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      54.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 115
    Processing helix  chain 'A' and resid 137 through 140
      removed outlier: 3.653A  pdb=" N   LYS A 140 " --> pdb=" O   GLN A 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 137 through 140'
    Processing helix  chain 'A' and resid 156 through 169
    Processing helix  chain 'A' and resid 174 through 181
    Processing helix  chain 'A' and resid 185 through 190
    Processing helix  chain 'A' and resid 210 through 219
      removed outlier: 4.183A  pdb=" N   SER A 216 " --> pdb=" O   ARG A 212 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A 218 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 252
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.890A  pdb=" N   PHE A 315 " --> pdb=" O   ASN A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 347
      removed outlier: 3.577A  pdb=" N   THR A 340 " --> pdb=" O   ASN A 336 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   THR A 347 " --> pdb=" O   THR A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 357
    Processing helix  chain 'A' and resid 381 through 401
      removed outlier: 3.594A  pdb=" N   LEU A 393 " --> pdb=" O   GLN A 389 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 3.637A  pdb=" N   TRP A 425 " --> pdb=" O   CYS A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 455
      removed outlier: 3.800A  pdb=" N   LEU A 439 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 456 through 458
      No H-bonds generated for 'chain 'A' and resid 456 through 458'
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 4.027A  pdb=" N   ARG A 468 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 489
      removed outlier: 3.756A  pdb=" N   ALA A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LEU A 486 " --> pdb=" O   MET A 482 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 506
      removed outlier: 3.878A  pdb=" N   ALA A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TRP A 505 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 540
      removed outlier: 3.627A  pdb=" N   PHE A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLY A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 561
      removed outlier: 3.993A  pdb=" N   THR A 549 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   VAL A 553 " --> pdb=" O   THR A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 580
      removed outlier: 4.185A  pdb=" N   VAL A 579 " --> pdb=" O   TRP A 575 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER A 580 " --> pdb=" O   MET A 576 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 575 through 580'
    Processing helix  chain 'A' and resid 581 through 595
      removed outlier: 3.807A  pdb=" N   CYS A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 604
    Processing helix  chain 'A' and resid 639 through 656
      removed outlier: 3.549A  pdb=" N   LEU A 644 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ARG A 650 " --> pdb=" O   PHE A 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 115
    Processing helix  chain 'B' and resid 137 through 140
      removed outlier: 3.652A  pdb=" N   LYS B 140 " --> pdb=" O   GLN B 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 137 through 140'
    Processing helix  chain 'B' and resid 156 through 169
    Processing helix  chain 'B' and resid 174 through 181
    Processing helix  chain 'B' and resid 185 through 190
    Processing helix  chain 'B' and resid 210 through 219
      removed outlier: 4.182A  pdb=" N   SER B 216 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA B 218 " --> pdb=" O   ARG B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 252
    Processing helix  chain 'B' and resid 297 through 301
    Processing helix  chain 'B' and resid 311 through 319
      removed outlier: 3.889A  pdb=" N   PHE B 315 " --> pdb=" O   ASN B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 347
      removed outlier: 3.578A  pdb=" N   THR B 340 " --> pdb=" O   ASN B 336 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   THR B 347 " --> pdb=" O   THR B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 357
    Processing helix  chain 'B' and resid 381 through 401
      removed outlier: 3.594A  pdb=" N   LEU B 393 " --> pdb=" O   GLN B 389 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 425
      removed outlier: 3.637A  pdb=" N   TRP B 425 " --> pdb=" O   CYS B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 455
      removed outlier: 3.799A  pdb=" N   LEU B 439 " --> pdb=" O   ASP B 435 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
      Proline residue:  B 451  - end of helix
    Processing helix  chain 'B' and resid 456 through 458
      No H-bonds generated for 'chain 'B' and resid 456 through 458'
    Processing helix  chain 'B' and resid 459 through 461
      No H-bonds generated for 'chain 'B' and resid 459 through 461'
    Processing helix  chain 'B' and resid 462 through 473
      removed outlier: 4.026A  pdb=" N   ARG B 468 " --> pdb=" O   ALA B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 489
      removed outlier: 3.756A  pdb=" N   ALA B 483 " --> pdb=" O   SER B 479 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS B 484 " --> pdb=" O   TYR B 480 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LEU B 486 " --> pdb=" O   MET B 482 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU B 489 " --> pdb=" O   VAL B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 506
      removed outlier: 3.878A  pdb=" N   ALA B 497 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   PHE B 502 " --> pdb=" O   SER B 498 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TRP B 505 " --> pdb=" O   THR B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 540
      removed outlier: 3.627A  pdb=" N   PHE B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY B 532 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLY B 534 " --> pdb=" O   SER B 530 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLY B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 561
      removed outlier: 3.994A  pdb=" N   THR B 549 " --> pdb=" O   LYS B 545 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE B 550 " --> pdb=" O   LYS B 546 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR B 552 " --> pdb=" O   SER B 548 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   VAL B 553 " --> pdb=" O   THR B 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 580
      removed outlier: 4.185A  pdb=" N   VAL B 579 " --> pdb=" O   TRP B 575 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B 580 " --> pdb=" O   MET B 576 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 575 through 580'
    Processing helix  chain 'B' and resid 581 through 595
      removed outlier: 3.807A  pdb=" N   CYS B 585 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 604
    Processing helix  chain 'B' and resid 639 through 656
      removed outlier: 3.548A  pdb=" N   LEU B 644 " --> pdb=" O   GLY B 640 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ARG B 650 " --> pdb=" O   PHE B 646 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 91
      removed outlier: 5.624A  pdb=" N   ARG A  81 " --> pdb=" O   LYS A  50 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   LYS A  50 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE A  83 " --> pdb=" O   ARG A  48 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ARG A  48 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER A  85 " --> pdb=" O   CYS A  46 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   CYS A  46 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   VAL A  87 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100
      removed outlier: 6.221A  pdb=" N   ALA A  98 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   LEU A 281 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU A 100 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL A 278 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL A 289 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU A 280 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145
      removed outlier: 6.242A  pdb=" N   GLY A 143 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   LEU A 228 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 91
      removed outlier: 5.623A  pdb=" N   ARG B  81 " --> pdb=" O   LYS B  50 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   LYS B  50 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ILE B  83 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ARG B  48 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER B  85 " --> pdb=" O   CYS B  46 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   CYS B  46 " --> pdb=" O   SER B  85 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   VAL B  87 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 100
      removed outlier: 6.221A  pdb=" N   ALA B  98 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   LEU B 281 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU B 100 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   VAL B 278 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU B 280 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145
      removed outlier: 6.242A  pdb=" N   GLY B 143 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU B 228 " --> pdb=" O   VAL B 261 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    356 hydrogen bonds defined for protein.
    1038 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: 1.33

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2103
        1.33 -     1.45: 1737
        1.45 -     1.57: 4894
        1.57 -     1.69: 10
        1.69 -     1.81: 86
  Bond restraints: 8830
  Sorted by residual:
  bond pdb=" C4  ATP B 701 "
       pdb=" C5  ATP B 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.462 -0.074 1.00e-02 1.00e+04 5.51e+01
  bond pdb=" C4  ATP A 701 "
       pdb=" C5  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.388  1.461 -0.073 1.00e-02 1.00e+04 5.33e+01
  bond pdb=" C5  ATP A 701 "
       pdb=" C6  ATP A 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.474 -0.065 1.00e-02 1.00e+04 4.17e+01
  bond pdb=" C5  ATP B 701 "
       pdb=" C6  ATP B 701 "
    ideal  model  delta    sigma   weight residual
    1.409  1.473 -0.064 1.00e-02 1.00e+04 4.13e+01
  bond pdb=" C5  ATP B 701 "
       pdb=" N7  ATP B 701 "
    ideal  model  delta    sigma   weight residual
    1.387  1.338  0.049 1.00e-02 1.00e+04 2.39e+01
  ... (remaining 8825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.83: 11812
        3.83 -     7.66: 140
        7.66 -    11.49: 24
       11.49 -    15.32: 0
       15.32 -    19.16: 4
  Bond angle restraints: 11980
  Sorted by residual:
  angle pdb=" PB  ATP B 701 "
        pdb=" O3B ATP B 701 "
        pdb=" PG  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     139.87  120.71   19.16 1.00e+00 1.00e+00 3.67e+02
  angle pdb=" PB  ATP A 701 "
        pdb=" O3B ATP A 701 "
        pdb=" PG  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     139.87  120.72   19.15 1.00e+00 1.00e+00 3.67e+02
  angle pdb=" PA  ATP A 701 "
        pdb=" O3A ATP A 701 "
        pdb=" PB  ATP A 701 "
      ideal   model   delta    sigma   weight residual
     136.83  120.55   16.28 1.00e+00 1.00e+00 2.65e+02
  angle pdb=" PA  ATP B 701 "
        pdb=" O3A ATP B 701 "
        pdb=" PB  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     136.83  120.55   16.28 1.00e+00 1.00e+00 2.65e+02
  angle pdb=" C5  ATP B 701 "
        pdb=" C4  ATP B 701 "
        pdb=" N3  ATP B 701 "
      ideal   model   delta    sigma   weight residual
     126.80  118.78    8.02 1.00e+00 1.00e+00 6.43e+01
  ... (remaining 11975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4683
       18.00 -    36.00: 473
       36.00 -    53.99: 48
       53.99 -    71.99: 18
       71.99 -    89.99: 4
  Dihedral angle restraints: 5226
    sinusoidal: 2074
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" CA  GLY B 104 "
           pdb=" C   GLY B 104 "
           pdb=" N   SER B 105 "
           pdb=" CA  SER B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.46  -25.54     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  GLY A 104 "
           pdb=" C   GLY A 104 "
           pdb=" N   SER A 105 "
           pdb=" CA  SER A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.47  -25.53     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  GLY B 631 "
           pdb=" C   GLY B 631 "
           pdb=" N   ASP B 632 "
           pdb=" CA  ASP B 632 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.31  -23.69     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 5223 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1136
       0.069 -    0.138: 247
       0.138 -    0.208: 31
       0.208 -    0.277: 8
       0.277 -    0.346: 4
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CB  ILE A 129 "
            pdb=" CA  ILE A 129 "
            pdb=" CG1 ILE A 129 "
            pdb=" CG2 ILE A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" CB  ILE B 129 "
            pdb=" CA  ILE B 129 "
            pdb=" CG1 ILE B 129 "
            pdb=" CG2 ILE B 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" CB  VAL B 199 "
            pdb=" CA  VAL B 199 "
            pdb=" CG1 VAL B 199 "
            pdb=" CG2 VAL B 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.72e+00
  ... (remaining 1423 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  51 "   -0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   ILE A  51 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ILE A  51 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   HIS A  52 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  51 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.95e+00
        pdb=" C   ILE B  51 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ILE B  51 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   HIS B  52 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 169 "    0.043 5.00e-02 4.00e+02   6.59e-02 6.94e+00
        pdb=" N   PRO A 170 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 170 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 170 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1981
        2.78 -     3.31: 7582
        3.31 -     3.84: 13599
        3.84 -     4.37: 16642
        4.37 -     4.90: 28822
  Nonbonded interactions: 68626
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 156 "
            pdb=" OE1 GLU A 159 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OG1 THR B 156 "
            pdb=" OE1 GLU B 159 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OH  TYR A 578 "
            pdb=" OD2 ASP A 632 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OH  TYR B 578 "
            pdb=" OD2 ASP B 632 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OE1 GLU B 469 "
            pdb=" OH  TYR B 475 "
     model   vdw
     2.330 3.040
  ... (remaining 68621 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
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:             1.820
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.060
  Find NCS groups from input model:        0.060
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
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      :  0.008   0.075   8830  Z= 0.401
  Angle     :  1.189  19.156  11980  Z= 0.754
  Chirality :  0.062   0.346   1426
  Planarity :  0.007   0.066   1452
  Dihedral  : 14.311  89.989   3198
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  6.94 %
    Favored  : 91.56 %
  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 aren not related in a simple way.
  whole: -5.42 (0.18), residues: 1076
  helix: -3.50 (0.13), residues: 614
  sheet: -2.64 (0.44), residues: 80
  loop : -3.65 (0.24), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.014   0.002   TYR A 594 
 PHE   0.020   0.002   PHE A 499 
 TRP   0.012   0.002   TRP A 426 
 HIS   0.013   0.002   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00807 ( 8830)
  covalent geometry    : angle       1.18908 (11980)
  hydrogen bonds       : bond        0.15313 (  356)
  hydrogen bonds       : angle       6.28686 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ASP cc_start: 0.8413 (t0) cc_final: 0.8055 (t70)
REVERT: A  462 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7553 (mm-30)
REVERT: B  231 ASP cc_start: 0.8421 (t0) cc_final: 0.8062 (t70)
REVERT: B  462 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7430 (mm-30)
REVERT: B  546 LYS cc_start: 0.7629 (mttt) cc_final: 0.7397 (mttm)
  outliers start: 14
  outliers final: 7
  residues processed: 137
  average time/residue: 0.0934
  time to fit residues: 17.2076
Evaluate side-chains
  94 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 THR
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain B residue   39 THR
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  342 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  52 HIS
A 112 ASN
A 395 HIS
B  52 HIS
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 395 HIS
B 427 HIS
B 434 HIS
B 567 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.161380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.121713 restraints weight = 10450.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.86
r_work: 0.3376 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8830  Z= 0.125
  Angle     :  0.600   7.651  11980  Z= 0.316
  Chirality :  0.042   0.190   1426
  Planarity :  0.005   0.060   1452
  Dihedral  :  8.589  82.218   1264
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 13.35 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.68 (0.22), residues: 1076
  helix: -1.91 (0.18), residues: 606
  sheet: -2.60 (0.54), residues: 60
  loop : -3.08 (0.25), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 401 
 TYR   0.016   0.001   TYR B 152 
 PHE   0.017   0.001   PHE A 315 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.006   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8830)
  covalent geometry    : angle       0.60008 (11980)
  hydrogen bonds       : bond        0.03221 (  356)
  hydrogen bonds       : angle       4.15849 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8961 (m-80) cc_final: 0.8313 (m-80)
REVERT: A  231 ASP cc_start: 0.8441 (t0) cc_final: 0.8096 (t70)
REVERT: A  286 CYS cc_start: 0.7949 (p) cc_final: 0.7483 (p)
REVERT: A  293 ARG cc_start: 0.6536 (mmt-90) cc_final: 0.5994 (mmp80)
REVERT: A  315 PHE cc_start: 0.6695 (t80) cc_final: 0.6195 (t80)
REVERT: A  462 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7580 (mm-30)
REVERT: A  492 GLU cc_start: 0.7625 (tp30) cc_final: 0.6435 (tp30)
REVERT: A  573 MET cc_start: 0.8438 (mtp) cc_final: 0.8196 (ttm)
REVERT: B  152 TYR cc_start: 0.8993 (m-80) cc_final: 0.8357 (m-80)
REVERT: B  183 GLU cc_start: 0.6806 (mp0) cc_final: 0.6573 (mp0)
REVERT: B  231 ASP cc_start: 0.8499 (t0) cc_final: 0.8188 (t70)
REVERT: B  462 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7576 (mm-30)
REVERT: B  492 GLU cc_start: 0.7600 (tp30) cc_final: 0.6362 (tp30)
REVERT: B  508 TYR cc_start: 0.7616 (t80) cc_final: 0.7349 (t80)
REVERT: B  573 MET cc_start: 0.8460 (ttm) cc_final: 0.8063 (ttm)
  outliers start: 7
  outliers final: 5
  residues processed: 113
  average time/residue: 0.1189
  time to fit residues: 17.9272
Evaluate side-chains
  98 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  280 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 86 optimal weight:    4.9990
   chunk 106 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 254 HIS
A 427 HIS
B 254 HIS
B 273 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.152728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.113286 restraints weight = 10732.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.77
r_work: 0.3276 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055   8830  Z= 0.328
  Angle     :  0.743   7.539  11980  Z= 0.380
  Chirality :  0.049   0.183   1426
  Planarity :  0.005   0.060   1452
  Dihedral  :  8.833  82.074   1256
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.49 %
    Favored  : 82.05 %
  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 aren not related in a simple way.
  whole: -3.42 (0.22), residues: 1076
  helix: -1.71 (0.19), residues: 610
  sheet: -2.48 (0.53), residues: 62
  loop : -2.98 (0.25), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 180 
 TYR   0.015   0.002   TYR B 565 
 PHE   0.019   0.002   PHE A 446 
 TRP   0.012   0.002   TRP B 447 
 HIS   0.007   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00811 ( 8830)
  covalent geometry    : angle       0.74271 (11980)
  hydrogen bonds       : bond        0.04245 (  356)
  hydrogen bonds       : angle       4.30229 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  286 CYS cc_start: 0.7907 (p) cc_final: 0.7483 (p)
REVERT: A  492 GLU cc_start: 0.7729 (tp30) cc_final: 0.6642 (tp30)
REVERT: A  573 MET cc_start: 0.8676 (mtp) cc_final: 0.8386 (ttm)
REVERT: B  231 ASP cc_start: 0.8612 (t0) cc_final: 0.8211 (t0)
REVERT: B  286 CYS cc_start: 0.7988 (p) cc_final: 0.7551 (p)
REVERT: B  492 GLU cc_start: 0.7605 (tp30) cc_final: 0.6624 (tp30)
REVERT: B  508 TYR cc_start: 0.7652 (t80) cc_final: 0.7437 (t80)
REVERT: B  573 MET cc_start: 0.8602 (ttm) cc_final: 0.8337 (ttm)
  outliers start: 23
  outliers final: 14
  residues processed: 114
  average time/residue: 0.0891
  time to fit residues: 14.8338
Evaluate side-chains
  102 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 23 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.162153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.123126 restraints weight = 10676.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.74
r_work: 0.3410 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8830  Z= 0.121
  Angle     :  0.556   7.215  11980  Z= 0.290
  Chirality :  0.041   0.142   1426
  Planarity :  0.004   0.056   1452
  Dihedral  :  8.232  84.352   1256
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.35 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.24), residues: 1076
  helix: -0.82 (0.21), residues: 596
  sheet: -2.26 (0.57), residues: 60
  loop : -2.47 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 401 
 TYR   0.008   0.001   TYR A 152 
 PHE   0.028   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 447 
 HIS   0.004   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8830)
  covalent geometry    : angle       0.55567 (11980)
  hydrogen bonds       : bond        0.02891 (  356)
  hydrogen bonds       : angle       3.83842 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8929 (m-80) cc_final: 0.8227 (m-80)
REVERT: A  231 ASP cc_start: 0.8524 (t0) cc_final: 0.8217 (t70)
REVERT: A  286 CYS cc_start: 0.7824 (p) cc_final: 0.7458 (p)
REVERT: A  462 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7360 (mm-30)
REVERT: A  492 GLU cc_start: 0.7507 (tp30) cc_final: 0.6475 (tp30)
REVERT: B  152 TYR cc_start: 0.8944 (m-80) cc_final: 0.8580 (m-80)
REVERT: B  231 ASP cc_start: 0.8564 (t0) cc_final: 0.8275 (t70)
REVERT: B  286 CYS cc_start: 0.7883 (p) cc_final: 0.7494 (p)
REVERT: B  462 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7564 (mm-30)
REVERT: B  492 GLU cc_start: 0.7491 (tp30) cc_final: 0.6506 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0780
  time to fit residues: 12.2622
Evaluate side-chains
  102 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0370
   chunk 94 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.1262

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

Flipped N/Q/H residues before XYZ refinement:
B 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.161270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.121945 restraints weight = 10587.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.74
r_work: 0.3396 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8830  Z= 0.141
  Angle     :  0.568   7.228  11980  Z= 0.290
  Chirality :  0.042   0.147   1426
  Planarity :  0.004   0.057   1452
  Dihedral  :  8.105  84.692   1256
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.63 %
    Favored  : 80.13 %
  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 aren not related in a simple way.
  whole: -1.91 (0.24), residues: 1076
  helix: -0.49 (0.21), residues: 598
  sheet: -1.97 (0.61), residues: 60
  loop : -2.25 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 158 
 TYR   0.009   0.001   TYR B 152 
 PHE   0.027   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 447 
 HIS   0.004   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8830)
  covalent geometry    : angle       0.56768 (11980)
  hydrogen bonds       : bond        0.03040 (  356)
  hydrogen bonds       : angle       3.74438 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  152 TYR cc_start: 0.8925 (m-80) cc_final: 0.8185 (m-80)
REVERT: A  231 ASP cc_start: 0.8588 (t0) cc_final: 0.8293 (t70)
REVERT: A  286 CYS cc_start: 0.7810 (p) cc_final: 0.7487 (p)
REVERT: A  409 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7768 (tt)
REVERT: A  462 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7269 (mm-30)
REVERT: A  492 GLU cc_start: 0.7451 (tp30) cc_final: 0.6418 (tp30)
REVERT: B  152 TYR cc_start: 0.8904 (m-80) cc_final: 0.8682 (m-80)
REVERT: B  231 ASP cc_start: 0.8579 (t0) cc_final: 0.8277 (t70)
REVERT: B  286 CYS cc_start: 0.7874 (p) cc_final: 0.7480 (p)
REVERT: B  409 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7778 (tt)
REVERT: B  492 GLU cc_start: 0.7405 (tp30) cc_final: 0.6442 (tp30)
  outliers start: 21
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0846
  time to fit residues: 13.6126
Evaluate side-chains
  109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  514 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.161613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122469 restraints weight = 10600.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.73
r_work: 0.3400 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8830  Z= 0.138
  Angle     :  0.559   7.168  11980  Z= 0.285
  Chirality :  0.041   0.142   1426
  Planarity :  0.004   0.055   1452
  Dihedral  :  7.961  84.736   1256
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.63 %
    Favored  : 79.81 %
  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 aren not related in a simple way.
  whole: -1.62 (0.25), residues: 1076
  helix: -0.27 (0.21), residues: 598
  sheet: -1.69 (0.66), residues: 60
  loop : -2.12 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 205 
 TYR   0.008   0.001   TYR A 152 
 PHE   0.031   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 447 
 HIS   0.004   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8830)
  covalent geometry    : angle       0.55897 (11980)
  hydrogen bonds       : bond        0.02961 (  356)
  hydrogen bonds       : angle       3.68888 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6626 (tpt) cc_final: 0.6022 (tpt)
REVERT: A  137 GLN cc_start: 0.8901 (mp10) cc_final: 0.8661 (mp10)
REVERT: A  152 TYR cc_start: 0.8893 (m-80) cc_final: 0.8177 (m-80)
REVERT: A  231 ASP cc_start: 0.8573 (t0) cc_final: 0.8247 (t70)
REVERT: A  286 CYS cc_start: 0.7798 (p) cc_final: 0.7480 (p)
REVERT: A  409 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7767 (tt)
REVERT: A  462 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7276 (mm-30)
REVERT: A  492 GLU cc_start: 0.7485 (tp30) cc_final: 0.6431 (tp30)
REVERT: B   97 MET cc_start: 0.6609 (tpt) cc_final: 0.5990 (tpt)
REVERT: B  137 GLN cc_start: 0.8892 (mp10) cc_final: 0.8656 (mp10)
REVERT: B  152 TYR cc_start: 0.8881 (m-80) cc_final: 0.8680 (m-80)
REVERT: B  231 ASP cc_start: 0.8577 (t0) cc_final: 0.8258 (t70)
REVERT: B  286 CYS cc_start: 0.7851 (p) cc_final: 0.7508 (p)
REVERT: B  409 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7800 (tt)
REVERT: B  492 GLU cc_start: 0.7421 (tp30) cc_final: 0.6438 (tp30)
REVERT: B  576 MET cc_start: 0.8334 (mtm) cc_final: 0.8082 (mtt)
  outliers start: 24
  outliers final: 19
  residues processed: 112
  average time/residue: 0.0855
  time to fit residues: 14.0379
Evaluate side-chains
  112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  633 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0070
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.7804

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

Flipped N/Q/H residues before XYZ refinement:
B 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.158738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.119301 restraints weight = 10735.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.74
r_work: 0.3361 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8830  Z= 0.196
  Angle     :  0.605   7.192  11980  Z= 0.308
  Chirality :  0.044   0.156   1426
  Planarity :  0.004   0.056   1452
  Dihedral  :  8.007  83.709   1256
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.99 %
    Favored  : 80.13 %
  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 aren not related in a simple way.
  whole: -1.85 (0.25), residues: 1076
  helix: -0.46 (0.21), residues: 616
  sheet: -1.53 (0.66), residues: 62
  loop : -2.32 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 470 
 TYR   0.009   0.001   TYR B 565 
 PHE   0.025   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 447 
 HIS   0.006   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8830)
  covalent geometry    : angle       0.60529 (11980)
  hydrogen bonds       : bond        0.03339 (  356)
  hydrogen bonds       : angle       3.84557 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6718 (tpt) cc_final: 0.6167 (tpt)
REVERT: A  137 GLN cc_start: 0.8868 (mp10) cc_final: 0.8625 (mp10)
REVERT: A  152 TYR cc_start: 0.8909 (m-80) cc_final: 0.8640 (m-80)
REVERT: A  231 ASP cc_start: 0.8539 (t0) cc_final: 0.8136 (t0)
REVERT: A  286 CYS cc_start: 0.7849 (p) cc_final: 0.7630 (p)
REVERT: A  409 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7767 (tt)
REVERT: A  492 GLU cc_start: 0.7400 (tp30) cc_final: 0.6322 (tp30)
REVERT: B   97 MET cc_start: 0.6679 (tpt) cc_final: 0.6164 (tpt)
REVERT: B  137 GLN cc_start: 0.8876 (mp10) cc_final: 0.8639 (mp10)
REVERT: B  152 TYR cc_start: 0.8911 (m-80) cc_final: 0.8626 (m-80)
REVERT: B  183 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6609 (mp0)
REVERT: B  231 ASP cc_start: 0.8551 (t0) cc_final: 0.8229 (t70)
REVERT: B  286 CYS cc_start: 0.7864 (p) cc_final: 0.7645 (p)
REVERT: B  288 PHE cc_start: 0.7420 (t80) cc_final: 0.7079 (t80)
REVERT: B  409 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7798 (tt)
REVERT: B  492 GLU cc_start: 0.7356 (tp30) cc_final: 0.6348 (tp30)
  outliers start: 27
  outliers final: 19
  residues processed: 114
  average time/residue: 0.0785
  time to fit residues: 13.4504
Evaluate side-chains
  113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  183 GLU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  273 GLN
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  633 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 106 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0370
   chunk 55 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 65 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0020
   overall best weight:    0.8868

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

Flipped N/Q/H residues before XYZ refinement:
A 273 GLN
B 273 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.162301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.123233 restraints weight = 10495.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.71
r_work: 0.3408 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8830  Z= 0.121
  Angle     :  0.547   7.883  11980  Z= 0.279
  Chirality :  0.041   0.141   1426
  Planarity :  0.004   0.054   1452
  Dihedral  :  7.824  84.706   1256
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.27 %
    Favored  : 79.17 %
  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 aren not related in a simple way.
  whole: -1.55 (0.25), residues: 1076
  helix: -0.17 (0.21), residues: 616
  sheet: -1.56 (0.68), residues: 60
  loop : -2.24 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 158 
 TYR   0.006   0.001   TYR B 152 
 PHE   0.023   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 447 
 HIS   0.004   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8830)
  covalent geometry    : angle       0.54699 (11980)
  hydrogen bonds       : bond        0.02794 (  356)
  hydrogen bonds       : angle       3.68802 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6671 (tpt) cc_final: 0.6058 (tpt)
REVERT: A  137 GLN cc_start: 0.8903 (mp10) cc_final: 0.8657 (mp10)
REVERT: A  152 TYR cc_start: 0.8902 (m-80) cc_final: 0.8646 (m-80)
REVERT: A  231 ASP cc_start: 0.8567 (t0) cc_final: 0.8241 (t70)
REVERT: A  286 CYS cc_start: 0.7786 (p) cc_final: 0.7464 (p)
REVERT: A  288 PHE cc_start: 0.7242 (t80) cc_final: 0.7025 (t80)
REVERT: A  409 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7794 (tt)
REVERT: A  492 GLU cc_start: 0.7351 (tp30) cc_final: 0.6277 (tp30)
REVERT: B   97 MET cc_start: 0.6673 (tpt) cc_final: 0.6064 (tpt)
REVERT: B  152 TYR cc_start: 0.8884 (m-80) cc_final: 0.8649 (m-80)
REVERT: B  159 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6513 (mp0)
REVERT: B  231 ASP cc_start: 0.8569 (t0) cc_final: 0.8246 (t70)
REVERT: B  288 PHE cc_start: 0.7354 (t80) cc_final: 0.7059 (t80)
REVERT: B  409 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7803 (tt)
REVERT: B  492 GLU cc_start: 0.7317 (tp30) cc_final: 0.6304 (tp30)
  outliers start: 24
  outliers final: 17
  residues processed: 116
  average time/residue: 0.0799
  time to fit residues: 13.9118
Evaluate side-chains
  111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  633 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.161270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.121923 restraints weight = 10558.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.74
r_work: 0.3394 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8830  Z= 0.150
  Angle     :  0.595   8.810  11980  Z= 0.298
  Chirality :  0.042   0.145   1426
  Planarity :  0.004   0.054   1452
  Dihedral  :  7.812  84.470   1256
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 18.38 %
    Favored  : 78.63 %
  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 aren not related in a simple way.
  whole: -1.47 (0.25), residues: 1076
  helix: -0.11 (0.21), residues: 616
  sheet: -1.53 (0.68), residues: 60
  loop : -2.19 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 158 
 TYR   0.007   0.001   TYR B 565 
 PHE   0.022   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 447 
 HIS   0.005   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8830)
  covalent geometry    : angle       0.59534 (11980)
  hydrogen bonds       : bond        0.03010 (  356)
  hydrogen bonds       : angle       3.70230 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6668 (tpt) cc_final: 0.6062 (tpt)
REVERT: A  137 GLN cc_start: 0.8897 (mp10) cc_final: 0.8652 (mp10)
REVERT: A  152 TYR cc_start: 0.8904 (m-80) cc_final: 0.8623 (m-80)
REVERT: A  159 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6499 (mp0)
REVERT: A  231 ASP cc_start: 0.8543 (t0) cc_final: 0.8220 (t70)
REVERT: A  288 PHE cc_start: 0.7290 (t80) cc_final: 0.7083 (t80)
REVERT: A  409 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7775 (tt)
REVERT: A  492 GLU cc_start: 0.7365 (tp30) cc_final: 0.6288 (tp30)
REVERT: B   97 MET cc_start: 0.6635 (tpt) cc_final: 0.6068 (tpt)
REVERT: B  152 TYR cc_start: 0.8898 (m-80) cc_final: 0.8633 (m-80)
REVERT: B  159 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6478 (mp0)
REVERT: B  231 ASP cc_start: 0.8545 (t0) cc_final: 0.8228 (t70)
REVERT: B  409 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7793 (tt)
REVERT: B  492 GLU cc_start: 0.7287 (tp30) cc_final: 0.6270 (tp30)
  outliers start: 28
  outliers final: 20
  residues processed: 113
  average time/residue: 0.0836
  time to fit residues: 14.0509
Evaluate side-chains
  111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  633 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.160635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121046 restraints weight = 10678.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.75
r_work: 0.3378 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8830  Z= 0.170
  Angle     :  0.606   8.951  11980  Z= 0.306
  Chirality :  0.043   0.149   1426
  Planarity :  0.004   0.055   1452
  Dihedral  :  7.871  84.024   1256
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.27 %
    Favored  : 78.85 %
  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 aren not related in a simple way.
  whole: -1.44 (0.25), residues: 1076
  helix: -0.11 (0.21), residues: 616
  sheet: -1.43 (0.66), residues: 62
  loop : -2.17 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 401 
 TYR   0.008   0.001   TYR B 565 
 PHE   0.025   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 447 
 HIS   0.005   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 8830)
  covalent geometry    : angle       0.60587 (11980)
  hydrogen bonds       : bond        0.03123 (  356)
  hydrogen bonds       : angle       3.77031 ( 1038)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   97 MET cc_start: 0.6678 (tpt) cc_final: 0.6144 (tpt)
REVERT: A  152 TYR cc_start: 0.8918 (m-80) cc_final: 0.8630 (m-80)
REVERT: A  159 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6429 (mp0)
REVERT: A  231 ASP cc_start: 0.8560 (t0) cc_final: 0.8150 (t0)
REVERT: A  286 CYS cc_start: 0.7822 (p) cc_final: 0.7484 (p)
REVERT: A  409 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7799 (tt)
REVERT: A  492 GLU cc_start: 0.7337 (tp30) cc_final: 0.6270 (tp30)
REVERT: B   97 MET cc_start: 0.6660 (tpt) cc_final: 0.6147 (tpt)
REVERT: B  152 TYR cc_start: 0.8894 (m-80) cc_final: 0.8622 (m-80)
REVERT: B  159 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6405 (mp0)
REVERT: B  231 ASP cc_start: 0.8565 (t0) cc_final: 0.8240 (t70)
REVERT: B  286 CYS cc_start: 0.7810 (p) cc_final: 0.7472 (p)
REVERT: B  409 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7818 (tt)
REVERT: B  492 GLU cc_start: 0.7277 (tp30) cc_final: 0.6262 (tp30)
  outliers start: 27
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0813
  time to fit residues: 13.7183
Evaluate side-chains
  115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  156 THR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue   36 PHE
Chi-restraints excluded: chain B residue   44 ASP
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  156 THR
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  633 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3980 r_free = 0.3980 target = 0.159037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118530 restraints weight = 10571.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.95
r_work: 0.3332 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8830  Z= 0.109
  Angle     :  0.551   8.441  11980  Z= 0.278
  Chirality :  0.040   0.136   1426
  Planarity :  0.004   0.053   1452
  Dihedral  :  7.700  85.138   1256
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.70 %
    Favored  : 78.95 %
  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 aren not related in a simple way.
  whole: -1.11 (0.26), residues: 1076
  helix:  0.18 (0.22), residues: 616
  sheet: -1.37 (0.69), residues: 60
  loop : -2.06 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 158 
 TYR   0.006   0.001   TYR B 152 
 PHE   0.025   0.001   PHE A 315 
 TRP   0.009   0.001   TRP B 447 
 HIS   0.004   0.000   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8830)
  covalent geometry    : angle       0.55133 (11980)
  hydrogen bonds       : bond        0.02673 (  356)
  hydrogen bonds       : angle       3.59575 ( 1038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1976.87 seconds
wall clock time: 34 minutes 48.48 seconds (2088.48 seconds total)