Starting phenix.real_space_refine
on Sat Aug 23 05:59:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8orh_17125/08_2025/8orh_17125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8orh_17125/08_2025/8orh_17125.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8orh_17125/08_2025/8orh_17125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8orh_17125/08_2025/8orh_17125.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8orh_17125/08_2025/8orh_17125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8orh_17125/08_2025/8orh_17125.cif"
  }
  resolution = 4.2
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      32      5.16       5
     C    6434      2.51       5
     N    1742      2.21       5
     O    1912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 10124
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 649, 5009
          Classifications: {'peptide': 649}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 39, 'TRANS': 609}
    Chain: "B"
      Number of atoms: 5009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 649, 5009
          Classifications: {'peptide': 649}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 39, 'TRANS': 609}
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.76, per 1000 atoms: 0.27
  Number of scatterers: 10124
  At special positions: 0
  Unit cell: (98.8169, 90.1297, 112.934, 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      32     16.00
     P       4     15.00
     O    1912      8.00
     N    1742      7.00
     C    6434      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: 0.97
  Conformation dependent library (CDL) restraints added in 400.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2360

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 15 sheets defined
      39.1% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 78
      removed outlier: 3.788A  pdb=" N   PHE A  78 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 100
    Processing helix  chain 'A' and resid 101 through 106
      removed outlier: 3.512A  pdb=" N   PHE A 104 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 154
    Processing helix  chain 'A' and resid 164 through 171
      removed outlier: 3.658A  pdb=" N   TRP A 171 " --> pdb=" O   PHE A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 179
    Processing helix  chain 'A' and resid 180 through 192
      removed outlier: 3.626A  pdb=" N   ARG A 186 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 221
      removed outlier: 4.190A  pdb=" N   SER A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 287
    Processing helix  chain 'A' and resid 299 through 303
    Processing helix  chain 'A' and resid 352 through 360
    Processing helix  chain 'A' and resid 364 through 372
    Processing helix  chain 'A' and resid 402 through 410
    Processing helix  chain 'A' and resid 460 through 468
    Processing helix  chain 'A' and resid 520 through 532
      removed outlier: 3.515A  pdb=" N   GLN A 524 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
      Proline residue:  A 526  - end of helix
    Processing helix  chain 'A' and resid 532 through 560
      removed outlier: 3.976A  pdb=" N   GLN A 554 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 586
      removed outlier: 3.546A  pdb=" N   ILE A 575 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 599
      removed outlier: 4.500A  pdb=" N   TRP A 590 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
      removed outlier: 3.817A  pdb=" N   GLY A 599 " --> pdb=" O   THR A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 616
    Processing helix  chain 'A' and resid 617 through 622
      removed outlier: 3.587A  pdb=" N   VAL A 621 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 659
    Processing helix  chain 'A' and resid 667 through 684
      removed outlier: 3.958A  pdb=" N   ALA A 671 " --> pdb=" O   THR A 667 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A 672 " --> pdb=" O   TRP A 668 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP A 680 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 691
    Processing helix  chain 'B' and resid 67 through 78
    Processing helix  chain 'B' and resid 95 through 100
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 110 through 114
      removed outlier: 4.217A  pdb=" N   ASN B 114 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 120
    Processing helix  chain 'B' and resid 149 through 154
      removed outlier: 3.549A  pdb=" N   MET B 153 " --> pdb=" O   GLY B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 170
    Processing helix  chain 'B' and resid 176 through 179
    Processing helix  chain 'B' and resid 180 through 192
    Processing helix  chain 'B' and resid 201 through 221
      removed outlier: 3.687A  pdb=" N   VAL B 205 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.753A  pdb=" N   THR B 232 " --> pdb=" O   ASN B 229 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLY B 233 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 229 through 233'
    Processing helix  chain 'B' and resid 281 through 287
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 351 through 361
      removed outlier: 4.215A  pdb=" N   THR B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 372
    Processing helix  chain 'B' and resid 402 through 410
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.975A  pdb=" N   ASN B 442 " --> pdb=" O   ALA B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 468
    Processing helix  chain 'B' and resid 520 through 532
      Proline residue:  B 526  - end of helix
    Processing helix  chain 'B' and resid 532 through 560
      removed outlier: 3.832A  pdb=" N   GLN B 554 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 586
    Processing helix  chain 'B' and resid 587 through 593
      removed outlier: 4.653A  pdb=" N   TRP B 590 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 599
      removed outlier: 3.750A  pdb=" N   GLY B 599 " --> pdb=" O   PRO B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 616
      removed outlier: 3.501A  pdb=" N   SER B 616 " --> pdb=" O   LEU B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 622
      removed outlier: 4.236A  pdb=" N   ARG B 620 " --> pdb=" O   SER B 616 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 659
    Processing helix  chain 'B' and resid 667 through 684
      removed outlier: 3.703A  pdb=" N   ASP B 680 " --> pdb=" O   ALA B 676 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 308
      removed outlier: 6.121A  pdb=" N   ILE A  83 " --> pdb=" O   ARG A 306 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   VAL A 308 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 11.348A  pdb=" N   THR A  56 " --> pdb=" O   ASN A 341 " (cutoff:3.500A)
      removed outlier: 10.980A  pdb=" N   GLU A 343 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ASP A  58 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   VAL A 345 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL A  60 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL A 340 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   VAL A 324 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ILE A 317 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   VAL A 326 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ARG A 315 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   TYR A 328 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL A 313 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 308
      removed outlier: 6.121A  pdb=" N   ILE A  83 " --> pdb=" O   ARG A 306 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   VAL A 308 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 11.348A  pdb=" N   THR A  56 " --> pdb=" O   ASN A 341 " (cutoff:3.500A)
      removed outlier: 10.980A  pdb=" N   GLU A 343 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ASP A  58 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   VAL A 345 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL A  60 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 128
      removed outlier: 3.689A  pdb=" N   HIS A 144 " --> pdb=" O   TRP A 125 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271
    Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 387
      removed outlier: 5.754A  pdb=" N   GLY A 490 " --> pdb=" O   GLY A 386 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 428
      removed outlier: 3.845A  pdb=" N   ALA A 426 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 481 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TYR A 391 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 426 through 428
      removed outlier: 3.845A  pdb=" N   ALA A 426 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 481 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TYR A 391 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER A 392 " --> pdb=" O   HIS A 624 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   HIS A 624 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 305 through 308
      removed outlier: 6.286A  pdb=" N   ILE B  83 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   VAL B 308 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU B  85 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ILE B  84 " --> pdb=" O   GLY B  57 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ILE B  59 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   LEU B  86 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ILE B  61 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 11.622A  pdb=" N   THR B  56 " --> pdb=" O   ASN B 341 " (cutoff:3.500A)
      removed outlier: 11.030A  pdb=" N   GLU B 343 " --> pdb=" O   THR B  56 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP B  58 " --> pdb=" O   GLU B 343 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   VAL B 345 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   VAL B  60 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   VAL B 324 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE B 317 " --> pdb=" O   VAL B 324 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   VAL B 326 " --> pdb=" O   ARG B 315 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ARG B 315 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   TYR B 328 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL B 313 " --> pdb=" O   TYR B 328 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 305 through 308
      removed outlier: 6.286A  pdb=" N   ILE B  83 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   VAL B 308 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU B  85 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ILE B  84 " --> pdb=" O   GLY B  57 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ILE B  59 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   LEU B  86 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ILE B  61 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 11.622A  pdb=" N   THR B  56 " --> pdb=" O   ASN B 341 " (cutoff:3.500A)
      removed outlier: 11.030A  pdb=" N   GLU B 343 " --> pdb=" O   THR B  56 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP B  58 " --> pdb=" O   GLU B 343 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   VAL B 345 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   VAL B  60 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 128
      removed outlier: 3.609A  pdb=" N   HIS B 144 " --> pdb=" O   TRP B 125 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 269 through 271
    Processing sheet with id=AB3, first strand: chain 'B' and resid 362 through 363
    Processing sheet with id=AB4, first strand: chain 'B' and resid 385 through 387
      removed outlier: 5.301A  pdb=" N   GLY B 490 " --> pdb=" O   GLY B 386 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 426 through 428
      removed outlier: 3.624A  pdb=" N   ALA B 426 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA B 481 " --> pdb=" O   PRO B 393 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR B 391 " --> pdb=" O   ASP B 483 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG B 398 " --> pdb=" O   GLU B 566 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 426 through 428
      removed outlier: 3.624A  pdb=" N   ALA B 426 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA B 481 " --> pdb=" O   PRO B 393 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR B 391 " --> pdb=" O   ASP B 483 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   SER B 392 " --> pdb=" O   HIS B 624 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   HIS B 624 " --> pdb=" O   SER B 392 " (cutoff:3.500A)

    391 hydrogen bonds defined for protein.
    1044 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: 1.88

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3331
        1.34 -     1.46: 1969
        1.46 -     1.57: 5016
        1.57 -     1.69: 4
        1.69 -     1.81: 60
  Bond restraints: 10380
  Sorted by residual:
  bond pdb=" O3P FAD A 901 "
       pdb=" P   FAD A 901 "
    ideal  model  delta    sigma   weight residual
    1.660  1.577  0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" O3P FAD B 901 "
       pdb=" P   FAD B 901 "
    ideal  model  delta    sigma   weight residual
    1.660  1.577  0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" O5B FAD A 901 "
       pdb=" PA  FAD A 901 "
    ideal  model  delta    sigma   weight residual
    1.634  1.565  0.069 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" O5' FAD B 901 "
       pdb=" P   FAD B 901 "
    ideal  model  delta    sigma   weight residual
    1.637  1.572  0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" O5' FAD A 901 "
       pdb=" P   FAD A 901 "
    ideal  model  delta    sigma   weight residual
    1.637  1.573  0.064 2.00e-02 2.50e+03 1.04e+01
  ... (remaining 10375 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 13866
        1.53 -     3.06: 252
        3.06 -     4.59: 41
        4.59 -     6.12: 11
        6.12 -     7.66: 8
  Bond angle restraints: 14178
  Sorted by residual:
  angle pdb=" N   ALA B 487 "
        pdb=" CA  ALA B 487 "
        pdb=" C   ALA B 487 "
      ideal   model   delta    sigma   weight residual
     109.81  116.02   -6.21 2.21e+00 2.05e-01 7.89e+00
  angle pdb=" O1P FAD A 901 "
        pdb=" P   FAD A 901 "
        pdb=" O2P FAD A 901 "
      ideal   model   delta    sigma   weight residual
     122.50  114.84    7.66 3.00e+00 1.11e-01 6.51e+00
  angle pdb=" C   MET B 567 "
        pdb=" N   VAL B 568 "
        pdb=" CA  VAL B 568 "
      ideal   model   delta    sigma   weight residual
     123.16  120.46    2.70 1.06e+00 8.90e-01 6.49e+00
  angle pdb=" N   ALA A 487 "
        pdb=" CA  ALA A 487 "
        pdb=" C   ALA A 487 "
      ideal   model   delta    sigma   weight residual
     109.81  115.42   -5.61 2.21e+00 2.05e-01 6.44e+00
  angle pdb=" O1A FAD B 901 "
        pdb=" PA  FAD B 901 "
        pdb=" O2A FAD B 901 "
      ideal   model   delta    sigma   weight residual
     121.20  113.91    7.29 3.00e+00 1.11e-01 5.91e+00
  ... (remaining 14173 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 5571
       17.52 -    35.05: 464
       35.05 -    52.57: 84
       52.57 -    70.09: 21
       70.09 -    87.62: 6
  Dihedral angle restraints: 6146
    sinusoidal: 2426
      harmonic: 3720
  Sorted by residual:
  dihedral pdb=" CA  ASN B 666 "
           pdb=" C   ASN B 666 "
           pdb=" N   THR B 667 "
           pdb=" CA  THR B 667 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.85  -18.15     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  ASN A 666 "
           pdb=" C   ASN A 666 "
           pdb=" N   THR A 667 "
           pdb=" CA  THR A 667 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.17  -17.83     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  VAL A 503 "
           pdb=" C   VAL A 503 "
           pdb=" N   PRO A 504 "
           pdb=" CA  PRO A 504 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.55   17.45     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 6143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 913
       0.031 -    0.063: 399
       0.063 -    0.094: 145
       0.094 -    0.125: 98
       0.125 -    0.157: 17
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" CA  ILE B 459 "
            pdb=" N   ILE B 459 "
            pdb=" C   ILE B 459 "
            pdb=" CB  ILE B 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.14e-01
  chirality pdb=" C2B FAD A 901 "
            pdb=" C1B FAD A 901 "
            pdb=" C3B FAD A 901 "
            pdb=" O2B FAD A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.69    0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" C2B FAD B 901 "
            pdb=" C1B FAD B 901 "
            pdb=" C3B FAD B 901 "
            pdb=" O2B FAD B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.68    0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 1569 not shown)

  Planarity restraints: 1844
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 402 "   -0.040 5.00e-02 4.00e+02   6.06e-02 5.88e+00
        pdb=" N   PRO B 403 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 403 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 403 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 569 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO B 570 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 570 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 570 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 569 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO A 570 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 570 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 570 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1841 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1747
        2.77 -     3.30: 9368
        3.30 -     3.83: 16573
        3.83 -     4.37: 19676
        4.37 -     4.90: 34634
  Nonbonded interactions: 81998
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 281 "
            pdb=" OG1 THR B 285 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   GLY A 149 "
            pdb=" OG1 THR A 152 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OE2 GLU B  87 "
            pdb=" O2B FAD B 901 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   GLY A 174 "
            pdb=" NH2 ARG A 677 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OE2 GLU A  87 "
            pdb=" O2B FAD A 901 "
     model   vdw
     2.263 3.040
  ... (remaining 81993 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.720
  Find NCS groups from input model:        0.160
  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:             0.010
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
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      :  0.004   0.083  10380  Z= 0.175
  Angle     :  0.557   7.656  14178  Z= 0.280
  Chirality :  0.047   0.157   1572
  Planarity :  0.005   0.061   1844
  Dihedral  : 13.568  87.616   3786
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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: -0.23 (0.24), residues: 1294
  helix:  0.52 (0.26), residues: 414
  sheet:  0.09 (0.40), residues: 202
  loop : -0.59 (0.24), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 606 
 TYR   0.009   0.001   TYR B 618 
 PHE   0.023   0.001   PHE B 486 
 TRP   0.009   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10380)
  covalent geometry    : angle       0.55687 (14178)
  hydrogen bonds       : bond        0.21717 (  360)
  hydrogen bonds       : angle       7.87025 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  216 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7248 (tm-30)
REVERT: B  216 GLN cc_start: 0.7497 (tt0) cc_final: 0.7270 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1575
  time to fit residues: 12.6517
Evaluate side-chains
  49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0270
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:   20.0000
   chunk 35 optimal weight:    7.9990
   overall best weight:    5.0046

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2413 r_free = 0.2413 target = 0.050293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2214 r_free = 0.2214 target = 0.042023 restraints weight = 27050.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2237 r_free = 0.2237 target = 0.042971 restraints weight = 17642.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2254 r_free = 0.2254 target = 0.043624 restraints weight = 13130.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2261 r_free = 0.2261 target = 0.043930 restraints weight = 10694.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2269 r_free = 0.2269 target = 0.044264 restraints weight = 9542.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.2267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10380  Z= 0.186
  Angle     :  0.603   7.096  14178  Z= 0.315
  Chirality :  0.050   0.160   1572
  Planarity :  0.005   0.051   1844
  Dihedral  :  6.061  74.525   1514
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  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: -0.25 (0.24), residues: 1294
  helix:  0.57 (0.26), residues: 404
  sheet: -0.08 (0.40), residues: 202
  loop : -0.58 (0.24), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 606 
 TYR   0.013   0.001   TYR B 491 
 PHE   0.025   0.002   PHE B 486 
 TRP   0.012   0.001   TRP A 125 
 HIS   0.004   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (10380)
  covalent geometry    : angle       0.60297 (14178)
  hydrogen bonds       : bond        0.05487 (  360)
  hydrogen bonds       : angle       5.49999 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7198 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1327
  time to fit residues: 9.9166
Evaluate side-chains
  48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 126 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 117 optimal weight:    7.9990
   chunk 110 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 169 ASN
A 379 ASN
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 524 GLN
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2422 r_free = 0.2422 target = 0.050702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2234 r_free = 0.2234 target = 0.042863 restraints weight = 26953.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2254 r_free = 0.2254 target = 0.043654 restraints weight = 18857.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2265 r_free = 0.2265 target = 0.044103 restraints weight = 14659.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2276 r_free = 0.2276 target = 0.044542 restraints weight = 12475.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2280 r_free = 0.2280 target = 0.044685 restraints weight = 11036.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.2278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10380  Z= 0.173
  Angle     :  0.590   7.359  14178  Z= 0.308
  Chirality :  0.050   0.175   1572
  Planarity :  0.005   0.052   1844
  Dihedral  :  5.906  76.166   1514
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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: -0.30 (0.24), residues: 1294
  helix:  0.61 (0.26), residues: 404
  sheet: -0.06 (0.40), residues: 192
  loop : -0.68 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 156 
 TYR   0.012   0.001   TYR B 491 
 PHE   0.019   0.002   PHE B 486 
 TRP   0.012   0.001   TRP A 125 
 HIS   0.004   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (10380)
  covalent geometry    : angle       0.59036 (14178)
  hydrogen bonds       : bond        0.05235 (  360)
  hydrogen bonds       : angle       5.29383 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7223 (tm-30)
REVERT: B  153 MET cc_start: 0.7653 (ttp) cc_final: 0.7365 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1384
  time to fit residues: 11.6160
Evaluate side-chains
  49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 81 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 99 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2443 r_free = 0.2443 target = 0.051419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2245 r_free = 0.2245 target = 0.043118 restraints weight = 26893.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2269 r_free = 0.2269 target = 0.044102 restraints weight = 17606.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2285 r_free = 0.2285 target = 0.044756 restraints weight = 13041.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2293 r_free = 0.2293 target = 0.045078 restraints weight = 10726.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2302 r_free = 0.2302 target = 0.045444 restraints weight = 9544.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.2300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10380  Z= 0.130
  Angle     :  0.546   6.738  14178  Z= 0.284
  Chirality :  0.048   0.162   1572
  Planarity :  0.005   0.049   1844
  Dihedral  :  5.714  77.389   1514
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  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:  0.01 (0.24), residues: 1294
  helix:  0.98 (0.27), residues: 382
  sheet: -0.01 (0.39), residues: 192
  loop : -0.48 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 606 
 TYR   0.012   0.001   TYR B 491 
 PHE   0.015   0.001   PHE B 486 
 TRP   0.010   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10380)
  covalent geometry    : angle       0.54566 (14178)
  hydrogen bonds       : bond        0.04453 (  360)
  hydrogen bonds       : angle       5.06699 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7207 (tm-30)
REVERT: B  153 MET cc_start: 0.7630 (ttp) cc_final: 0.7421 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1239
  time to fit residues: 10.3434
Evaluate side-chains
  50 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 126 optimal weight:   10.0000
   chunk 117 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 54 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 78 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 524 GLN
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2434 r_free = 0.2434 target = 0.051031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2235 r_free = 0.2235 target = 0.042690 restraints weight = 27179.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2259 r_free = 0.2259 target = 0.043657 restraints weight = 17692.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2273 r_free = 0.2273 target = 0.044243 restraints weight = 13121.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2286 r_free = 0.2286 target = 0.044782 restraints weight = 10827.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2291 r_free = 0.2291 target = 0.044972 restraints weight = 9294.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.2289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10380  Z= 0.143
  Angle     :  0.553   6.879  14178  Z= 0.287
  Chirality :  0.048   0.163   1572
  Planarity :  0.005   0.046   1844
  Dihedral  :  5.706  76.959   1514
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  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:  0.02 (0.24), residues: 1294
  helix:  1.02 (0.27), residues: 382
  sheet: -0.04 (0.39), residues: 192
  loop : -0.48 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 606 
 TYR   0.012   0.001   TYR B 491 
 PHE   0.014   0.001   PHE B 486 
 TRP   0.011   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (10380)
  covalent geometry    : angle       0.55344 (14178)
  hydrogen bonds       : bond        0.04579 (  360)
  hydrogen bonds       : angle       5.02308 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7234 (tm-30)
REVERT: B  153 MET cc_start: 0.7643 (ttp) cc_final: 0.7407 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1299
  time to fit residues: 9.8790
Evaluate side-chains
  48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 91 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 114 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2392 r_free = 0.2392 target = 0.049300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2188 r_free = 0.2188 target = 0.040933 restraints weight = 27629.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2212 r_free = 0.2212 target = 0.041846 restraints weight = 18244.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2229 r_free = 0.2229 target = 0.042499 restraints weight = 13756.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2238 r_free = 0.2238 target = 0.042857 restraints weight = 11220.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2246 r_free = 0.2246 target = 0.043160 restraints weight = 9915.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.2244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  10380  Z= 0.266
  Angle     :  0.679   8.533  14178  Z= 0.353
  Chirality :  0.053   0.192   1572
  Planarity :  0.006   0.051   1844
  Dihedral  :  6.236  77.641   1514
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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: -0.39 (0.23), residues: 1294
  helix:  0.59 (0.26), residues: 396
  sheet: -0.11 (0.39), residues: 192
  loop : -0.76 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 156 
 TYR   0.015   0.002   TYR A 465 
 PHE   0.028   0.002   PHE A 486 
 TRP   0.017   0.002   TRP A 125 
 HIS   0.006   0.002   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00660 (10380)
  covalent geometry    : angle       0.67901 (14178)
  hydrogen bonds       : bond        0.06005 (  360)
  hydrogen bonds       : angle       5.29759 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7277 (tm-30)
REVERT: B  153 MET cc_start: 0.7763 (ttp) cc_final: 0.7510 (ttp)
REVERT: B  567 MET cc_start: 0.8342 (ttm) cc_final: 0.8118 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1557
  time to fit residues: 12.3320
Evaluate side-chains
  47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0270
   chunk 5 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 126 optimal weight:    9.9990
   overall best weight:    4.0046

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2420 r_free = 0.2420 target = 0.050459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2222 r_free = 0.2222 target = 0.042202 restraints weight = 27019.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2245 r_free = 0.2245 target = 0.043117 restraints weight = 17672.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2260 r_free = 0.2260 target = 0.043710 restraints weight = 13251.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2272 r_free = 0.2272 target = 0.044160 restraints weight = 10939.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2276 r_free = 0.2276 target = 0.044337 restraints weight = 9563.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.2274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10380  Z= 0.157
  Angle     :  0.587   7.621  14178  Z= 0.305
  Chirality :  0.049   0.183   1572
  Planarity :  0.005   0.051   1844
  Dihedral  :  5.959  78.704   1514
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  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: -0.28 (0.23), residues: 1294
  helix:  0.72 (0.27), residues: 396
  sheet: -0.08 (0.39), residues: 192
  loop : -0.70 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 606 
 TYR   0.012   0.001   TYR B 491 
 PHE   0.022   0.002   PHE A 486 
 TRP   0.012   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (10380)
  covalent geometry    : angle       0.58668 (14178)
  hydrogen bonds       : bond        0.04942 (  360)
  hydrogen bonds       : angle       5.09141 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7267 (tm-30)
REVERT: B  153 MET cc_start: 0.7696 (ttp) cc_final: 0.7434 (ttp)
REVERT: B  567 MET cc_start: 0.8280 (ttm) cc_final: 0.8057 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1298
  time to fit residues: 10.6087
Evaluate side-chains
  47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 109 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2406 r_free = 0.2406 target = 0.049854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2208 r_free = 0.2208 target = 0.041633 restraints weight = 27027.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2231 r_free = 0.2231 target = 0.042571 restraints weight = 17684.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2248 r_free = 0.2248 target = 0.043226 restraints weight = 13151.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2256 r_free = 0.2256 target = 0.043547 restraints weight = 10694.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2264 r_free = 0.2264 target = 0.043890 restraints weight = 9539.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.2262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10380  Z= 0.208
  Angle     :  0.633   7.913  14178  Z= 0.330
  Chirality :  0.051   0.202   1572
  Planarity :  0.005   0.050   1844
  Dihedral  :  6.082  78.271   1514
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.23), residues: 1294
  helix:  0.63 (0.26), residues: 396
  sheet: -0.13 (0.39), residues: 192
  loop : -0.74 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 606 
 TYR   0.013   0.002   TYR A 465 
 PHE   0.026   0.002   PHE A 486 
 TRP   0.014   0.001   TRP A 125 
 HIS   0.004   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 (10380)
  covalent geometry    : angle       0.63309 (14178)
  hydrogen bonds       : bond        0.05419 (  360)
  hydrogen bonds       : angle       5.18980 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.426 
Fit side-chains
REVERT: B  153 MET cc_start: 0.7742 (ttp) cc_final: 0.7486 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1236
  time to fit residues: 10.1166
Evaluate side-chains
  46 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 116 optimal weight:    9.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2436 r_free = 0.2436 target = 0.051147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2240 r_free = 0.2240 target = 0.042892 restraints weight = 26786.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2265 r_free = 0.2265 target = 0.043876 restraints weight = 17337.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2281 r_free = 0.2281 target = 0.044543 restraints weight = 12786.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2293 r_free = 0.2293 target = 0.045000 restraints weight = 10393.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2298 r_free = 0.2298 target = 0.045211 restraints weight = 8962.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.2296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10380  Z= 0.128
  Angle     :  0.562   6.877  14178  Z= 0.292
  Chirality :  0.048   0.161   1572
  Planarity :  0.005   0.051   1844
  Dihedral  :  5.815  78.905   1514
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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: -0.04 (0.24), residues: 1294
  helix:  0.95 (0.27), residues: 382
  sheet: -0.03 (0.40), residues: 192
  loop : -0.52 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 606 
 TYR   0.012   0.001   TYR B 491 
 PHE   0.020   0.001   PHE A 486 
 TRP   0.010   0.001   TRP A 125 
 HIS   0.005   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10380)
  covalent geometry    : angle       0.56161 (14178)
  hydrogen bonds       : bond        0.04437 (  360)
  hydrogen bonds       : angle       4.99179 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.421 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1251
  time to fit residues: 9.7467
Evaluate side-chains
  49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 115 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 55 optimal weight:    9.9990
   chunk 112 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   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 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2435 r_free = 0.2435 target = 0.051109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2238 r_free = 0.2238 target = 0.042794 restraints weight = 26482.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2261 r_free = 0.2261 target = 0.043721 restraints weight = 17298.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2276 r_free = 0.2276 target = 0.044337 restraints weight = 12941.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2283 r_free = 0.2283 target = 0.044600 restraints weight = 10647.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2292 r_free = 0.2292 target = 0.044997 restraints weight = 9615.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10380  Z= 0.135
  Angle     :  0.564   6.800  14178  Z= 0.292
  Chirality :  0.048   0.162   1572
  Planarity :  0.005   0.051   1844
  Dihedral  :  5.770  78.403   1514
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  0.02 (0.24), residues: 1294
  helix:  0.99 (0.27), residues: 382
  sheet: -0.00 (0.40), residues: 188
  loop : -0.47 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 606 
 TYR   0.012   0.001   TYR B 491 
 PHE   0.020   0.001   PHE A 486 
 TRP   0.011   0.001   TRP A 125 
 HIS   0.004   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (10380)
  covalent geometry    : angle       0.56399 (14178)
  hydrogen bonds       : bond        0.04467 (  360)
  hydrogen bonds       : angle       4.94470 ( 1044)

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

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

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2588 Ramachandran restraints generated.
    1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.425 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1198
  time to fit residues: 9.1345
Evaluate side-chains
  48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.3980
   chunk 62 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   overall best weight:    4.0788

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2425 r_free = 0.2425 target = 0.050678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2227 r_free = 0.2227 target = 0.042399 restraints weight = 27000.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2250 r_free = 0.2250 target = 0.043308 restraints weight = 17417.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2265 r_free = 0.2265 target = 0.043918 restraints weight = 12952.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2277 r_free = 0.2277 target = 0.044386 restraints weight = 10631.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2280 r_free = 0.2280 target = 0.044506 restraints weight = 9273.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.2277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10380  Z= 0.156
  Angle     :  0.579   7.229  14178  Z= 0.301
  Chirality :  0.049   0.174   1572
  Planarity :  0.005   0.051   1844
  Dihedral  :  5.842  78.135   1514
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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: -0.02 (0.24), residues: 1294
  helix:  0.96 (0.27), residues: 382
  sheet:  0.01 (0.40), residues: 192
  loop : -0.51 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 606 
 TYR   0.012   0.001   TYR B 491 
 PHE   0.021   0.002   PHE A 486 
 TRP   0.012   0.001   TRP A 125 
 HIS   0.004   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (10380)
  covalent geometry    : angle       0.57867 (14178)
  hydrogen bonds       : bond        0.04716 (  360)
  hydrogen bonds       : angle       4.94638 ( 1044)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1374.07 seconds
wall clock time: 24 minutes 50.74 seconds (1490.74 seconds total)