Starting phenix.real_space_refine
on Sat Nov 16 02:11:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orh_17125/11_2024/8orh_17125.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orh_17125/11_2024/8orh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orh_17125/11_2024/8orh_17125.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orh_17125/11_2024/8orh_17125.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orh_17125/11_2024/8orh_17125.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orh_17125/11_2024/8orh_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.24, per 1000 atoms: 0.81
  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: 2.51
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.57
  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: 3.46

  Time building geometry restraints manager: 2.92 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: 0.00
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:             2.870
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     28.340
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.920
-------------------------------------------------------------------------------
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= 0.254
  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 

*********************** 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  : 1.151 
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: 0.3236
  time to fit residues: 26.3632
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  : 1.182 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.0714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10380  Z= 0.143
  Angle     :  0.515   5.664  14178  Z= 0.270
  Chirality :  0.046   0.148   1572
  Planarity :  0.005   0.049   1844
  Dihedral  :  6.023  74.348   1514
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  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 

*********************** 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  : 1.208 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7610 (tm-30) cc_final: 0.7214 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2837
  time to fit residues: 23.6769
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  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 32 optimal weight:   20.0000
   chunk 116 optimal weight:    0.9990
   chunk 125 optimal weight:    4.9990
   chunk 103 optimal weight:   10.0000
   chunk 115 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    3.1388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.0866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10380  Z= 0.205
  Angle     :  0.539   6.226  14178  Z= 0.280
  Chirality :  0.048   0.171   1572
  Planarity :  0.005   0.052   1844
  Dihedral  :  5.693  73.497   1514
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  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 (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:  0.09 (0.24), residues: 1294
  helix:  1.01 (0.27), residues: 390
  sheet: -0.02 (0.39), residues: 202
  loop : -0.40 (0.24), residues: 702

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   0.020   0.001   PHE B 486 
 TYR   0.011   0.001   TYR B 491 
 ARG   0.005   0.000   ARG A 606 

*********************** 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
  59 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.189 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7170 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2832
  time to fit residues: 23.7004
Evaluate side-chains
  51 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 116 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 110 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10380  Z= 0.266
  Angle     :  0.577   7.175  14178  Z= 0.299
  Chirality :  0.049   0.166   1572
  Planarity :  0.005   0.049   1844
  Dihedral  :  5.723  73.869   1514
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  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: -0.03 (0.24), residues: 1294
  helix:  0.92 (0.27), residues: 390
  sheet: -0.00 (0.39), residues: 192
  loop : -0.51 (0.24), residues: 712

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

*********************** 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
  57 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7201 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2561
  time to fit residues: 20.9533
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  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 70 optimal weight:    7.9990
   chunk 1 optimal weight:   20.0000
   chunk 92 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 105 optimal weight:    0.0070
   chunk 85 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 111 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    3.6006

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

Flipped N/Q/H residues before XYZ refinement:
B 666 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10380  Z= 0.228
  Angle     :  0.549   6.955  14178  Z= 0.285
  Chirality :  0.048   0.159   1572
  Planarity :  0.005   0.047   1844
  Dihedral  :  5.667  75.072   1514
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.77 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.06 (0.27), residues: 382
  sheet: -0.21 (0.38), residues: 202
  loop : -0.41 (0.24), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 
 PHE   0.015   0.002   PHE B 486 
 TYR   0.012   0.001   TYR B 491 
 ARG   0.005   0.000   ARG A 637 

*********************** 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
  58 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7200 (tm-30)
REVERT: B  153 MET cc_start: 0.7678 (ttp) cc_final: 0.7450 (ttp)
REVERT: B  216 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7289 (tt0)
REVERT: B  666 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7793 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2556
  time to fit residues: 21.6838
Evaluate side-chains
  49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 111 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 123 optimal weight:    5.9990
   chunk 102 optimal weight:   10.0000
   chunk 57 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   overall best weight:    2.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1134

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= 0.168
  Angle     :  0.519   6.390  14178  Z= 0.269
  Chirality :  0.047   0.150   1572
  Planarity :  0.004   0.045   1844
  Dihedral  :  5.520  77.064   1514
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.08 (0.24), residues: 1294
  helix:  1.08 (0.27), residues: 390
  sheet: -0.21 (0.38), residues: 198
  loop : -0.39 (0.24), residues: 706

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   0.017   0.001   PHE A 486 
 TYR   0.011   0.001   TYR B 491 
 ARG   0.005   0.000   ARG A 156 

*********************** 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
  56 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.178 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7192 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2749
  time to fit residues: 22.2736
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  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 119 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 70 optimal weight:    0.1980
   chunk 90 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0060
   chunk 123 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0470
   chunk 75 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.4498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10380  Z= 0.123
  Angle     :  0.484   5.455  14178  Z= 0.251
  Chirality :  0.045   0.148   1572
  Planarity :  0.004   0.046   1844
  Dihedral  :  5.260  76.723   1514
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.26 (0.24), residues: 1294
  helix:  1.20 (0.27), residues: 390
  sheet: -0.06 (0.39), residues: 198
  loop : -0.28 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 125 
 HIS   0.005   0.001   HIS B 591 
 PHE   0.014   0.001   PHE A 486 
 TYR   0.010   0.001   TYR B 618 
 ARG   0.004   0.000   ARG A 606 

*********************** 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
  59 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 1.187 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7065 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2649
  time to fit residues: 22.6499
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  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 24 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    0.2980
   chunk 84 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10380  Z= 0.133
  Angle     :  0.490   5.477  14178  Z= 0.252
  Chirality :  0.046   0.164   1572
  Planarity :  0.004   0.045   1844
  Dihedral  :  5.167  75.741   1514
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  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:  0.34 (0.24), residues: 1294
  helix:  1.30 (0.27), residues: 390
  sheet: -0.03 (0.39), residues: 198
  loop : -0.24 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 125 
 HIS   0.004   0.001   HIS B 144 
 PHE   0.014   0.001   PHE A 486 
 TYR   0.010   0.001   TYR B 491 
 ARG   0.003   0.000   ARG A 606 

*********************** 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  : 1.090 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7422 (tm-30) cc_final: 0.7051 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2781
  time to fit residues: 22.7125
Evaluate side-chains
  45 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   chunk 114 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 121 optimal weight:    0.6980
   overall best weight:    2.5388

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10380  Z= 0.184
  Angle     :  0.527   6.222  14178  Z= 0.271
  Chirality :  0.047   0.169   1572
  Planarity :  0.004   0.046   1844
  Dihedral  :  5.291  74.774   1514
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.24), residues: 1294
  helix:  1.31 (0.27), residues: 390
  sheet: -0.07 (0.39), residues: 198
  loop : -0.23 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.018   0.001   PHE A 486 
 TYR   0.011   0.001   TYR B 491 
 ARG   0.003   0.000   ARG A 306 

*********************** 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
  56 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.252 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7089 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.2858
  time to fit residues: 22.6300
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  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 127 optimal weight:    9.9990
   chunk 117 optimal weight:    0.8980
   chunk 101 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 78 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 80 optimal weight:   20.0000
   chunk 108 optimal weight:    9.9990
   overall best weight:    3.0986

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10380  Z= 0.209
  Angle     :  0.541   6.590  14178  Z= 0.278
  Chirality :  0.048   0.166   1572
  Planarity :  0.005   0.046   1844
  Dihedral  :  5.418  74.657   1514
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.31 (0.24), residues: 1294
  helix:  1.26 (0.27), residues: 390
  sheet:  0.09 (0.40), residues: 188
  loop : -0.29 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 125 
 HIS   0.003   0.001   HIS B  73 
 PHE   0.020   0.001   PHE A 486 
 TYR   0.012   0.001   TYR B 491 
 ARG   0.007   0.000   ARG A 606 

********************** 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
  55 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.220 
Fit side-chains
REVERT: A  216 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7176 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.2568
  time to fit residues: 20.3469
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  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 101 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   chunk 104 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0980
   overall best weight:    2.4186

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2469 r_free = 0.2469 target = 0.052443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2287 r_free = 0.2287 target = 0.044640 restraints weight = 26384.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2307 r_free = 0.2307 target = 0.045439 restraints weight = 18366.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2321 r_free = 0.2321 target = 0.046007 restraints weight = 14211.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.2319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1260

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= 0.177
  Angle     :  0.521   6.415  14178  Z= 0.268
  Chirality :  0.047   0.163   1572
  Planarity :  0.004   0.046   1844
  Dihedral  :  5.370  74.725   1514
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  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:  0.33 (0.24), residues: 1294
  helix:  1.30 (0.27), residues: 390
  sheet:  0.10 (0.40), residues: 188
  loop : -0.29 (0.24), residues: 716

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   0.019   0.001   PHE A 486 
 TYR   0.011   0.001   TYR B 491 
 ARG   0.008   0.000   ARG A 606 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1755.98 seconds
wall clock time: 33 minutes 16.48 seconds (1996.48 seconds total)