Starting phenix.real_space_refine
on Mon Jul 28 07:19:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8orh_17125/07_2025/8orh_17125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8orh_17125/07_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_17125/07_2025/8orh_17125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8orh_17125/07_2025/8orh_17125.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8orh_17125/07_2025/8orh_17125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8orh_17125/07_2025/8orh_17125.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 15.32, per 1000 atoms: 1.51
  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: 3.14
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.68
  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: 3.44

  Time building geometry restraints manager: 3.65 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: 0.05
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:             275.370
  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:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     38.990
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.050
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  318.460
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (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
 TRP   0.009   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.023   0.001   PHE B 486 
 TYR   0.009   0.001   TYR B 618 
 ARG   0.006   0.000   ARG A 606 

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

*********************** 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  : 1.223 
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: 0.3176
  time to fit residues: 25.9633
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  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0060
   chunk 61 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9990
   overall best weight:    1.2802

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.2466 r_free = 0.2466 target = 0.052534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2273 r_free = 0.2273 target = 0.044320 restraints weight = 26327.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2298 r_free = 0.2298 target = 0.045311 restraints weight = 17112.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2312 r_free = 0.2312 target = 0.045898 restraints weight = 12599.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.2309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.0713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10380  Z= 0.103
  Angle     :  0.515   5.661  14178  Z= 0.270
  Chirality :  0.046   0.148   1572
  Planarity :  0.005   0.049   1844
  Dihedral  :  6.023  74.352   1514
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1294
  helix:  0.78 (0.26), residues: 404
  sheet:  0.07 (0.40), residues: 198
  loop : -0.46 (0.24), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 125 
 HIS   0.002   0.001   HIS B  73 
 PHE   0.017   0.001   PHE B 486 
 TYR   0.011   0.001   TYR B 592 
 ARG   0.004   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  360)
  hydrogen bonds       : angle       5.39395 ( 1044)
  covalent geometry    : bond        0.00219 (10380)
  covalent geometry    : angle       0.51512 (14178)

*********************** 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
  59 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.098 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7217 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2676
  time to fit residues: 22.2234
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  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 36 optimal weight:    0.0570
   chunk 121 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0070
   chunk 59 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0170
   chunk 71 optimal weight:    8.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    1.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 666 ASN ** 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 = 0.2476 r_free = 0.2476 target = 0.052985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2285 r_free = 0.2285 target = 0.044711 restraints weight = 26319.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2310 r_free = 0.2310 target = 0.045726 restraints weight = 16973.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2325 r_free = 0.2325 target = 0.046362 restraints weight = 12507.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.2323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10380  Z= 0.097
  Angle     :  0.501   5.506  14178  Z= 0.260
  Chirality :  0.046   0.162   1572
  Planarity :  0.004   0.050   1844
  Dihedral  :  5.658  73.380   1514
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.24), residues: 1294
  helix:  1.08 (0.27), residues: 390
  sheet:  0.05 (0.39), residues: 198
  loop : -0.34 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 125 
 HIS   0.002   0.001   HIS B  73 
 PHE   0.016   0.001   PHE B 486 
 TYR   0.010   0.001   TYR B 491 
 ARG   0.006   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  360)
  hydrogen bonds       : angle       5.07351 ( 1044)
  covalent geometry    : bond        0.00216 (10380)
  covalent geometry    : angle       0.50110 (14178)

*********************** 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
  58 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.196 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7166 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2989
  time to fit residues: 25.6213
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  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 64 optimal weight:   20.0000
   chunk 76 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0170
   chunk 105 optimal weight:   10.0000
   chunk 89 optimal weight:    0.7980
   overall best weight:    1.7622

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.053152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2290 r_free = 0.2290 target = 0.044815 restraints weight = 26238.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2314 r_free = 0.2314 target = 0.045804 restraints weight = 17144.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2331 r_free = 0.2331 target = 0.046490 restraints weight = 12717.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.2328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10380  Z= 0.100
  Angle     :  0.502   5.495  14178  Z= 0.258
  Chirality :  0.046   0.153   1572
  Planarity :  0.004   0.047   1844
  Dihedral  :  5.396  72.082   1514
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.85 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1294
  helix:  1.15 (0.27), residues: 390
  sheet:  0.02 (0.39), residues: 198
  loop : -0.32 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 
 PHE   0.016   0.001   PHE B 486 
 TYR   0.011   0.001   TYR B 491 
 ARG   0.005   0.000   ARG A 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  360)
  hydrogen bonds       : angle       4.88385 ( 1044)
  covalent geometry    : bond        0.00229 (10380)
  covalent geometry    : angle       0.50154 (14178)

*********************** 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
  62 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 1.129 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7122 (tm-30)
REVERT: B  216 GLN cc_start: 0.7478 (tp-100) cc_final: 0.7248 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2674
  time to fit residues: 23.4644
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  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 121 optimal weight:    7.9990
   chunk 20 optimal weight:   20.0000
   chunk 86 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0670
   chunk 9 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   overall best weight:    4.2126

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

Flipped N/Q/H residues before XYZ refinement:
A 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2435 r_free = 0.2435 target = 0.051139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2238 r_free = 0.2238 target = 0.042829 restraints weight = 26747.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2262 r_free = 0.2262 target = 0.043796 restraints weight = 17537.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2278 r_free = 0.2278 target = 0.044454 restraints weight = 13029.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.2277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1050

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= 0.160
  Angle     :  0.563   7.198  14178  Z= 0.290
  Chirality :  0.049   0.165   1572
  Planarity :  0.005   0.046   1844
  Dihedral  :  5.579  72.436   1514
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.34
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.24), residues: 1294
  helix:  1.06 (0.27), residues: 390
  sheet: -0.12 (0.39), residues: 202
  loop : -0.39 (0.24), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 125 
 HIS   0.004   0.001   HIS B  73 
 PHE   0.019   0.002   PHE A 365 
 TYR   0.012   0.001   TYR B 491 
 ARG   0.004   0.000   ARG A 637 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 (  360)
  hydrogen bonds       : angle       4.92716 ( 1044)
  covalent geometry    : bond        0.00391 (10380)
  covalent geometry    : angle       0.56268 (14178)

*********************** 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  : 1.173 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7218 (tm-30)
REVERT: B  216 GLN cc_start: 0.7602 (tp-100) cc_final: 0.7314 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2974
  time to fit residues: 23.1807
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  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 102 optimal weight:    9.9990
   chunk 101 optimal weight:   20.0000
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 105 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    6.1990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2407 r_free = 0.2407 target = 0.049981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2220 r_free = 0.2220 target = 0.042161 restraints weight = 27133.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2238 r_free = 0.2238 target = 0.042899 restraints weight = 18681.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2252 r_free = 0.2252 target = 0.043433 restraints weight = 14635.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.2248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10380  Z= 0.216
  Angle     :  0.626   8.149  14178  Z= 0.325
  Chirality :  0.051   0.169   1572
  Planarity :  0.005   0.047   1844
  Dihedral  :  5.945  75.225   1514
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.24), residues: 1294
  helix:  0.95 (0.27), residues: 382
  sheet: -0.11 (0.39), residues: 192
  loop : -0.54 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 125 
 HIS   0.005   0.001   HIS A 336 
 PHE   0.018   0.002   PHE A 365 
 TYR   0.013   0.002   TYR A 465 
 ARG   0.004   0.000   ARG B 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05432 (  360)
  hydrogen bonds       : angle       5.06451 ( 1044)
  covalent geometry    : bond        0.00533 (10380)
  covalent geometry    : angle       0.62601 (14178)

*********************** 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
  57 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7273 (tm-30)
REVERT: B  153 MET cc_start: 0.7758 (ttp) cc_final: 0.7459 (ttp)
REVERT: B  567 MET cc_start: 0.8280 (ttm) cc_final: 0.8014 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.3393
  time to fit residues: 26.7239
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  : 2.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 83 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 125 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 182 ASN
** A 523 GLN ** 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 = 0.2411 r_free = 0.2411 target = 0.050121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2223 r_free = 0.2223 target = 0.042297 restraints weight = 27294.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2242 r_free = 0.2242 target = 0.043053 restraints weight = 18754.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2255 r_free = 0.2255 target = 0.043579 restraints weight = 14690.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.2253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10380  Z= 0.212
  Angle     :  0.624   7.948  14178  Z= 0.325
  Chirality :  0.051   0.188   1572
  Planarity :  0.005   0.052   1844
  Dihedral  :  6.046  79.030   1514
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.23), residues: 1294
  helix:  0.71 (0.26), residues: 396
  sheet: -0.18 (0.39), residues: 192
  loop : -0.71 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 125 
 HIS   0.005   0.001   HIS A 336 
 PHE   0.019   0.002   PHE A 486 
 TYR   0.013   0.002   TYR A 491 
 ARG   0.007   0.001   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05389 (  360)
  hydrogen bonds       : angle       5.07329 ( 1044)
  covalent geometry    : bond        0.00527 (10380)
  covalent geometry    : angle       0.62376 (14178)

*********************** 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
  56 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.730 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7275 (tm-30)
REVERT: B  153 MET cc_start: 0.7705 (ttp) cc_final: 0.7423 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.3227
  time to fit residues: 25.9464
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  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 66 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 124 optimal weight:    2.9990
   overall best weight:    4.3388

-------------------------------------------------------------------------------
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 216 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2423 r_free = 0.2423 target = 0.050618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2224 r_free = 0.2224 target = 0.042295 restraints weight = 27329.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2249 r_free = 0.2249 target = 0.043287 restraints weight = 17670.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2266 r_free = 0.2266 target = 0.043959 restraints weight = 12965.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1145

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= 0.164
  Angle     :  0.591   7.490  14178  Z= 0.308
  Chirality :  0.050   0.178   1572
  Planarity :  0.005   0.049   1844
  Dihedral  :  5.944  79.935   1514
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.23), residues: 1294
  helix:  0.78 (0.27), residues: 396
  sheet: -0.17 (0.39), residues: 192
  loop : -0.67 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 125 
 HIS   0.004   0.001   HIS B  73 
 PHE   0.024   0.002   PHE A 486 
 TYR   0.013   0.001   TYR B 618 
 ARG   0.006   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04938 (  360)
  hydrogen bonds       : angle       4.98509 ( 1044)
  covalent geometry    : bond        0.00405 (10380)
  covalent geometry    : angle       0.59112 (14178)

*********************** 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
  58 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.099 
Fit side-chains
REVERT: B  153 MET cc_start: 0.7655 (ttp) cc_final: 0.7380 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2313
  time to fit residues: 19.7211
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  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 126 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 83 optimal weight:    0.0000
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    3.7992

-------------------------------------------------------------------------------
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 = 0.2431 r_free = 0.2431 target = 0.050907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2245 r_free = 0.2245 target = 0.043111 restraints weight = 26945.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2263 r_free = 0.2263 target = 0.043849 restraints weight = 18497.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2278 r_free = 0.2278 target = 0.044451 restraints weight = 14483.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.2275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10380  Z= 0.150
  Angle     :  0.575   7.198  14178  Z= 0.299
  Chirality :  0.049   0.166   1572
  Planarity :  0.005   0.052   1844
  Dihedral  :  5.845  79.908   1514
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.24), residues: 1294
  helix:  1.00 (0.27), residues: 382
  sheet: -0.16 (0.39), residues: 192
  loop : -0.55 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 125 
 HIS   0.004   0.001   HIS B  73 
 PHE   0.023   0.002   PHE A 486 
 TYR   0.013   0.001   TYR B 491 
 ARG   0.006   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04687 (  360)
  hydrogen bonds       : angle       4.94161 ( 1044)
  covalent geometry    : bond        0.00366 (10380)
  covalent geometry    : angle       0.57518 (14178)

*********************** 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
  52 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 3.516 
Fit side-chains
REVERT: B  153 MET cc_start: 0.7667 (ttp) cc_final: 0.7461 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.3115
  time to fit residues: 23.9065
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  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 121 optimal weight:    0.0970
   chunk 125 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    2.6984

-------------------------------------------------------------------------------
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 = 0.2446 r_free = 0.2446 target = 0.051559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2248 r_free = 0.2248 target = 0.043180 restraints weight = 26795.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2273 r_free = 0.2273 target = 0.044196 restraints weight = 17145.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2290 r_free = 0.2290 target = 0.044878 restraints weight = 12547.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.2289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
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   0.027  10380  Z= 0.123
  Angle     :  0.549   6.715  14178  Z= 0.285
  Chirality :  0.048   0.163   1572
  Planarity :  0.005   0.053   1844
  Dihedral  :  5.716  79.951   1514
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.24), residues: 1294
  helix:  1.11 (0.27), residues: 382
  sheet: -0.01 (0.39), residues: 188
  loop : -0.51 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 
 PHE   0.021   0.001   PHE A 486 
 TYR   0.012   0.001   TYR B 491 
 ARG   0.006   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04282 (  360)
  hydrogen bonds       : angle       4.83984 ( 1044)
  covalent geometry    : bond        0.00295 (10380)
  covalent geometry    : angle       0.54936 (14178)

********************** 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
  54 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.678 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.3410
  time to fit residues: 26.6060
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  : 1.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 37 optimal weight:    9.9990
   chunk 72 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 106 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.2468 r_free = 0.2468 target = 0.052495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2278 r_free = 0.2278 target = 0.044329 restraints weight = 26496.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2302 r_free = 0.2302 target = 0.045293 restraints weight = 16952.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2318 r_free = 0.2318 target = 0.045951 restraints weight = 12550.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.2316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10380  Z= 0.103
  Angle     :  0.520   6.094  14178  Z= 0.268
  Chirality :  0.046   0.161   1572
  Planarity :  0.005   0.055   1844
  Dihedral  :  5.484  79.973   1514
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.24
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.24), residues: 1294
  helix:  1.24 (0.27), residues: 382
  sheet: -0.06 (0.39), residues: 188
  loop : -0.39 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 
 PHE   0.019   0.001   PHE A 486 
 TYR   0.011   0.001   TYR B 491 
 ARG   0.006   0.000   ARG A 606 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  360)
  hydrogen bonds       : angle       4.66302 ( 1044)
  covalent geometry    : bond        0.00241 (10380)
  covalent geometry    : angle       0.52024 (14178)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3023.36 seconds
wall clock time: 56 minutes 6.92 seconds (3366.92 seconds total)