Starting phenix.real_space_refine
on Mon Sep 23 17:27:49 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/09_2024/7p6a_13223.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/09_2024/7p6a_13223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/09_2024/7p6a_13223.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/09_2024/7p6a_13223.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/09_2024/7p6a_13223.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6a_13223/09_2024/7p6a_13223.cif"
  }
  resolution = 1.9
  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=   0.000 sd=   0.004
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: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2555      2.51       5
     N     765      2.21       5
     O     836      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 4166
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 818
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
      Conformer: "B"
        Number of residues, atoms: 108, 812
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
          bond proxies already assigned to first conformer: 816
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "B"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 20
          Classifications: {'water': 20}
          Link IDs: {None: 19}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "D"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 20
          Classifications: {'water': 20}
          Link IDs: {None: 19}
    Chain: "E"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.85, per 1000 atoms: 0.68
  Number of scatterers: 4166
  At special positions: 0
  Unit cell: (105.415, 82.878, 39.985, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     836      8.00
     N     765      7.00
     C    2555      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 908.6 milliseconds
  

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 51.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 292
      removed outlier: 6.322A  pdb=" N   VAL B 275 " --> pdb=" O   GLN C 276 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   ILE C 278 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ILE B 277 " --> pdb=" O   ILE C 278 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   LYS C 280 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ASN B 279 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   LEU C 282 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LYS B 281 " --> pdb=" O   LEU C 282 " (cutoff:3.500A)
      removed outlier: 9.381A  pdb=" N   LEU C 284 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
      removed outlier: 8.662A  pdb=" N   ASP B 283 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 10.022A  pdb=" N   ASN C 286 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   SER B 285 " --> pdb=" O   ASN C 286 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   GLN C 288 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL B 287 " --> pdb=" O   GLN C 288 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   LYS C 290 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   SER B 289 " --> pdb=" O   LYS C 290 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   GLY C 292 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   CYS B 291 " --> pdb=" O   GLY C 292 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   VAL A 275 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   ILE B 278 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE A 277 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   LYS B 280 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASN A 279 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU B 282 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   LYS A 281 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 9.369A  pdb=" N   LEU B 284 " --> pdb=" O   LYS A 281 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   ASP A 283 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 10.009A  pdb=" N   ASN B 286 " --> pdb=" O   ASP A 283 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   SER A 285 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   GLN B 288 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL A 287 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   LYS B 290 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   SER A 289 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   GLY B 292 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   CYS A 291 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU A 282 " --> pdb=" O   LYS D 281 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASP D 283 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LEU A 284 " --> pdb=" O   ASP D 283 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   SER D 285 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASN A 286 " --> pdb=" O   SER D 285 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   LEU D 282 " --> pdb=" O   LYS E 281 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASP E 283 " --> pdb=" O   LEU D 282 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU D 284 " --> pdb=" O   ASP E 283 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   SER E 285 " --> pdb=" O   LEU D 284 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ASN D 286 " --> pdb=" O   SER E 285 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 298
      removed outlier: 6.329A  pdb=" N   ILE B 297 " --> pdb=" O   LYS C 298 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ILE A 297 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 305 through 310
      removed outlier: 6.623A  pdb=" N   SER A 305 " --> pdb=" O   VAL D 306 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   ILE D 308 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLN A 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   TYR D 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   SER D 305 " --> pdb=" O   VAL E 306 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   ILE E 308 " --> pdb=" O   SER D 305 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   GLN D 307 " --> pdb=" O   ILE E 308 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   TYR E 310 " --> pdb=" O   GLN D 307 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL D 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314
      removed outlier: 6.758A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   VAL D 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 322
      removed outlier: 6.263A  pdb=" N   VAL B 318 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LYS C 321 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   SER B 320 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   VAL A 318 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LYS B 321 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   SER A 320 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 330
      removed outlier: 6.414A  pdb=" N   ILE B 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ILE A 328 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 337 through 340
      removed outlier: 6.339A  pdb=" N   VAL B 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   LYS C 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL B 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 343 through 346
      removed outlier: 6.441A  pdb=" N   LEU A 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU D 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 349 through 354
      removed outlier: 6.525A  pdb=" N   VAL A 350 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   LYS D 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   SER A 352 " --> pdb=" O   LYS D 353 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL D 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   LYS E 353 " --> pdb=" O   VAL D 350 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   SER D 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362
      removed outlier: 8.704A  pdb=" N   LEU B 357 " --> pdb=" O   ASP C 358 " (cutoff:3.500A)
      removed outlier: 9.580A  pdb=" N   ILE C 360 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASN B 359 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   HIS C 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   THR B 361 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
      removed outlier: 8.705A  pdb=" N   LEU A 357 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 9.582A  pdb=" N   ILE B 360 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ASN A 359 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   HIS B 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   THR A 361 " --> pdb=" O   HIS B 362 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ASP A 358 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASN D 359 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASP D 358 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ASN E 359 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 369 through 378
      removed outlier: 6.288A  pdb=" N   LYS B 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 8.772A  pdb=" N   GLU C 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ILE B 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   HIS C 374 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR B 373 " --> pdb=" O   HIS C 374 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   LEU C 376 " --> pdb=" O   THR B 373 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LYS B 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   PHE C 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   THR B 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 8.776A  pdb=" N   GLU B 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ILE A 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   HIS B 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   THR A 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   LEU B 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LYS A 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N   PHE B 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   LYS A 370 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LYS D 370 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)

    96 hydrogen bonds defined for protein.
    288 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 1.09 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: 1354
        1.34 -     1.46: 678
        1.46 -     1.58: 2108
        1.58 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 4150
  Sorted by residual:
  bond pdb=" N   SER A 285 "
       pdb=" CA  SER A 285 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.032 1.23e-02 6.61e+03 6.64e+00
  bond pdb=" N   LEU D 284 "
       pdb=" CA  LEU D 284 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.21e-02 6.83e+03 6.40e+00
  bond pdb=" N   LEU E 284 "
       pdb=" CA  LEU E 284 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.21e-02 6.83e+03 6.39e+00
  bond pdb=" N   LEU C 284 "
       pdb=" CA  LEU C 284 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.21e-02 6.83e+03 6.25e+00
  bond pdb=" N   LEU B 284 "
       pdb=" CA  LEU B 284 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.21e-02 6.83e+03 6.18e+00
  ... (remaining 4145 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 5187
        1.26 -     2.52: 283
        2.52 -     3.78: 49
        3.78 -     5.04: 21
        5.04 -     6.29: 5
  Bond angle restraints: 5545
  Sorted by residual:
  angle pdb=" N   SER B 285 "
        pdb=" CA  SER B 285 "
        pdb=" C   SER B 285 "
      ideal   model   delta    sigma   weight residual
     108.79  113.80   -5.01 1.53e+00 4.27e-01 1.07e+01
  angle pdb=" N   SER D 285 "
        pdb=" CA  SER D 285 "
        pdb=" C   SER D 285 "
      ideal   model   delta    sigma   weight residual
     108.79  113.79   -5.00 1.53e+00 4.27e-01 1.07e+01
  angle pdb=" N   SER E 285 "
        pdb=" CA  SER E 285 "
        pdb=" C   SER E 285 "
      ideal   model   delta    sigma   weight residual
     108.79  113.78   -4.99 1.53e+00 4.27e-01 1.06e+01
  angle pdb=" N   SER C 285 "
        pdb=" CA  SER C 285 "
        pdb=" C   SER C 285 "
      ideal   model   delta    sigma   weight residual
     108.79  113.75   -4.96 1.53e+00 4.27e-01 1.05e+01
  angle pdb=" N   SER A 285 "
        pdb=" CA  SER A 285 "
        pdb=" C   SER A 285 "
      ideal   model   delta    sigma   weight residual
     108.79  113.74   -4.95 1.53e+00 4.27e-01 1.05e+01
  ... (remaining 5540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 2360
       15.94 -    31.88: 155
       31.88 -    47.82: 40
       47.82 -    63.76: 5
       63.76 -    79.70: 5
  Dihedral angle restraints: 2565
    sinusoidal: 1075
      harmonic: 1490
  Sorted by residual:
  dihedral pdb=" CB  GLU D 372 "
           pdb=" CG  GLU D 372 "
           pdb=" CD  GLU D 372 "
           pdb=" OE1 GLU D 372 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.70   79.70     1      3.00e+01 1.11e-03 8.76e+00
  dihedral pdb=" CB  GLU B 372 "
           pdb=" CG  GLU B 372 "
           pdb=" CD  GLU B 372 "
           pdb=" OE1 GLU B 372 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.68   79.68     1      3.00e+01 1.11e-03 8.76e+00
  dihedral pdb=" CB  GLU A 372 "
           pdb=" CG  GLU A 372 "
           pdb=" CD  GLU A 372 "
           pdb=" OE1 GLU A 372 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.67   79.67     1      3.00e+01 1.11e-03 8.75e+00
  ... (remaining 2562 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 409
       0.047 -    0.095: 108
       0.095 -    0.142: 91
       0.142 -    0.190: 7
       0.190 -    0.237: 5
  Chirality restraints: 620
  Sorted by residual:
  chirality pdb=" CG  LEU D 282 "
            pdb=" CB  LEU D 282 "
            pdb=" CD1 LEU D 282 "
            pdb=" CD2 LEU D 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CG  LEU B 282 "
            pdb=" CB  LEU B 282 "
            pdb=" CD1 LEU B 282 "
            pdb=" CD2 LEU B 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CG  LEU C 282 "
            pdb=" CB  LEU C 282 "
            pdb=" CD1 LEU C 282 "
            pdb=" CD2 LEU C 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 617 not shown)

  Planarity restraints: 710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 349 "    0.121 9.50e-02 1.11e+02   5.44e-02 2.27e+00
        pdb=" NE  ARG C 349 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 349 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 349 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 349 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 349 "    0.122 9.50e-02 1.11e+02   5.48e-02 2.25e+00
        pdb=" NE  ARG B 349 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 349 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 349 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 349 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 349 "    0.121 9.50e-02 1.11e+02   5.44e-02 2.25e+00
        pdb=" NE  ARG E 349 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 349 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 349 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 349 "    0.001 2.00e-02 2.50e+03
  ... (remaining 707 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 463
        2.78 -     3.31: 3710
        3.31 -     3.84: 7626
        3.84 -     4.37: 8842
        4.37 -     4.90: 16483
  Nonbonded interactions: 37124
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 357 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OD1 ASP D 358 "
            pdb=" O   HOH D 501 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OD1 ASP B 358 "
            pdb=" O   HOH B 502 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" O   LEU C 357 "
            pdb=" O   HOH B 502 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" O   ASP D 295 "
            pdb=" OH  TYR D 310 "
     model   vdw
     2.372 3.040
  ... (remaining 37119 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' and (resid 272 through 342 or resid 344 through 379))
  selection = (chain 'B' and (resid 272 through 342 or resid 344 through 379))
  selection = (chain 'C' and (resid 272 through 342 or resid 344 through 379))
  selection = (chain 'D' and (resid 272 through 342 or resid 344 through 379))
  selection = (chain 'E' and (resid 272 through 342 or resid 344 through 379))
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.560
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
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   0.032   4150  Z= 0.245
  Angle     :  0.718   6.294   5545  Z= 0.415
  Chirality :  0.059   0.237    620
  Planarity :  0.006   0.055    710
  Dihedral  : 12.298  79.700   1625
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  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: -3.07 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.19), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D 374 
 PHE   0.006   0.001   PHE D 378 
 TYR   0.005   0.002   TYR B 310 
 ARG   0.012   0.003   ARG C 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.517 
Fit side-chains
REVERT: E  349 ARG cc_start: 0.7127 (mtt-85) cc_final: 0.6911 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.8708
  time to fit residues: 103.8801
Evaluate side-chains
  94 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 21 optimal weight:    0.3980
   chunk 12 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    3.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 330 HIS
B 276 GLN
B 330 HIS
D 276 GLN
E 276 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   4150  Z= 0.378
  Angle     :  0.662   7.217   5545  Z= 0.341
  Chirality :  0.055   0.175    620
  Planarity :  0.004   0.061    710
  Dihedral  :  6.025  15.000    560
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  5.32 %
    Favored  : 93.83 %
  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: -2.73 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS A 330 
 PHE   0.010   0.002   PHE E 378 
 TYR   0.006   0.002   TYR C 310 
 ARG   0.006   0.001   ARG D 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6924 (mtm180)
REVERT: A  356 SER cc_start: 0.8704 (t) cc_final: 0.8370 (p)
REVERT: E  349 ARG cc_start: 0.7314 (mtt-85) cc_final: 0.7112 (mtm180)
  outliers start: 4
  outliers final: 2
  residues processed: 106
  average time/residue: 0.8628
  time to fit residues: 95.8127
Evaluate side-chains
  101 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 279 ASN
A 330 HIS
B 276 GLN
D 276 GLN
D 279 ASN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4150  Z= 0.281
  Angle     :  0.602   6.845   5545  Z= 0.310
  Chirality :  0.053   0.141    620
  Planarity :  0.004   0.039    710
  Dihedral  :  5.930  15.278    560
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  7.02 %
    Favored  : 92.13 %
  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: -2.74 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.001   HIS A 330 
 PHE   0.008   0.002   PHE E 378 
 TYR   0.006   0.002   TYR C 310 
 ARG   0.003   0.001   ARG D 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A  356 SER cc_start: 0.8710 (t) cc_final: 0.8393 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 104
  average time/residue: 0.8365
  time to fit residues: 91.1666
Evaluate side-chains
  98 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 330 HIS
B 276 GLN
B 279 ASN
D 276 GLN
D 279 ASN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4150  Z= 0.286
  Angle     :  0.602   7.006   5545  Z= 0.311
  Chirality :  0.053   0.145    620
  Planarity :  0.003   0.024    710
  Dihedral  :  5.939  15.414    560
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.30 %
    Favored  : 91.06 %
  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: -2.73 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS A 330 
 PHE   0.007   0.001   PHE E 378 
 TYR   0.006   0.002   TYR C 310 
 ARG   0.002   0.000   ARG D 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A  356 SER cc_start: 0.8703 (t) cc_final: 0.8391 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 96
  average time/residue: 0.8394
  time to fit residues: 84.5518
Evaluate side-chains
  95 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 279 ASN
A 330 HIS
B 276 GLN
D 276 GLN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   4150  Z= 0.415
  Angle     :  0.663   7.443   5545  Z= 0.346
  Chirality :  0.054   0.179    620
  Planarity :  0.004   0.023    710
  Dihedral  :  6.192  16.104    560
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  8.51 %
    Favored  : 91.06 %
  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: -2.60 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.001   HIS A 330 
 PHE   0.009   0.002   PHE E 378 
 TYR   0.006   0.002   TYR E 310 
 ARG   0.003   0.001   ARG D 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  356 SER cc_start: 0.8726 (t) cc_final: 0.8386 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 100
  average time/residue: 0.8682
  time to fit residues: 90.9855
Evaluate side-chains
  100 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0370
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.6066

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
B 276 GLN
B 279 ASN
C 276 GLN
D 276 GLN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4150  Z= 0.214
  Angle     :  0.572   7.044   5545  Z= 0.293
  Chirality :  0.052   0.139    620
  Planarity :  0.003   0.023    710
  Dihedral  :  5.846  15.621    560
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  8.72 %
    Favored  : 90.21 %
  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: -2.70 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.001   HIS A 330 
 PHE   0.006   0.001   PHE E 378 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.002   0.001   ARG A 379 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  356 SER cc_start: 0.8707 (t) cc_final: 0.8415 (p)
REVERT: C  349 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6633 (mtp180)
  outliers start: 5
  outliers final: 1
  residues processed: 102
  average time/residue: 0.8464
  time to fit residues: 90.5666
Evaluate side-chains
  98 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 40 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
A 330 HIS
B 276 GLN
C 276 GLN
D 276 GLN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4150  Z= 0.278
  Angle     :  0.606   7.507   5545  Z= 0.312
  Chirality :  0.053   0.189    620
  Planarity :  0.003   0.023    710
  Dihedral  :  5.939  15.456    560
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.00 %
    Favored  : 88.94 %
  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: -2.67 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.001   HIS A 330 
 PHE   0.007   0.001   PHE E 378 
 TYR   0.006   0.002   TYR C 310 
 ARG   0.002   0.000   ARG D 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 SER cc_start: 0.8720 (t) cc_final: 0.8399 (p)
REVERT: C  349 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6591 (mtp180)
  outliers start: 5
  outliers final: 1
  residues processed: 101
  average time/residue: 0.8790
  time to fit residues: 92.9521
Evaluate side-chains
  99 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.7362

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
B 279 ASN
D 276 GLN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4150  Z= 0.223
  Angle     :  0.582   7.406   5545  Z= 0.297
  Chirality :  0.053   0.183    620
  Planarity :  0.003   0.023    710
  Dihedral  :  5.813  15.266    560
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 10.43 %
    Favored  : 88.94 %
  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: -2.71 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS A 330 
 PHE   0.006   0.001   PHE E 378 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.002   0.001   ARG A 379 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  356 SER cc_start: 0.8715 (t) cc_final: 0.8421 (p)
REVERT: C  349 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6591 (mtp180)
  outliers start: 3
  outliers final: 1
  residues processed: 101
  average time/residue: 0.8840
  time to fit residues: 93.5676
Evaluate side-chains
  100 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
D 276 GLN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4150  Z= 0.358
  Angle     :  0.649   7.658   5545  Z= 0.337
  Chirality :  0.056   0.248    620
  Planarity :  0.003   0.023    710
  Dihedral  :  6.081  15.669    560
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 11.06 %
    Favored  : 88.51 %
  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: -2.60 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.001   HIS A 330 
 PHE   0.008   0.002   PHE E 378 
 TYR   0.005   0.002   TYR E 310 
 ARG   0.002   0.000   ARG D 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.547 
Fit side-chains
REVERT: A  356 SER cc_start: 0.8730 (t) cc_final: 0.8392 (p)
REVERT: C  349 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6631 (mtp180)
  outliers start: 2
  outliers final: 1
  residues processed: 101
  average time/residue: 0.8615
  time to fit residues: 91.1896
Evaluate side-chains
  102 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   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 330 HIS
B 279 ASN
D 276 GLN
D 279 ASN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4150  Z= 0.418
  Angle     :  0.681   7.737   5545  Z= 0.355
  Chirality :  0.057   0.279    620
  Planarity :  0.004   0.025    710
  Dihedral  :  6.230  16.254    560
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 11.28 %
    Favored  : 88.30 %
  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: -2.55 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.001   HIS A 330 
 PHE   0.009   0.002   PHE B 378 
 TYR   0.006   0.002   TYR E 310 
 ARG   0.002   0.001   ARG D 349 

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

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

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1070 Ramachandran restraints generated.
    535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.520 
Fit side-chains
REVERT: A  356 SER cc_start: 0.8736 (t) cc_final: 0.8402 (p)
REVERT: C  349 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6875 (mpp-170)
  outliers start: 2
  outliers final: 1
  residues processed: 101
  average time/residue: 0.9155
  time to fit residues: 96.7519
Evaluate side-chains
  102 residues out of total 460 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 HIS
Chi-restraints excluded: chain C residue  349 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   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 330 HIS
D 276 GLN
E 276 GLN
E 279 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.126946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.109561 restraints weight = 16583.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.30
r_work: 0.3594 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3494 r_free = 0.3494    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3494
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   4150  Z= 0.419
  Angle     :  0.685   7.711   5545  Z= 0.356
  Chirality :  0.057   0.290    620
  Planarity :  0.004   0.031    710
  Dihedral  :  6.286  16.474    560
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 11.28 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.53 (0.26), residues: 535
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.20), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.001   HIS A 330 
 PHE   0.010   0.002   PHE E 378 
 TYR   0.006   0.002   TYR E 310 
 ARG   0.003   0.001   ARG D 349 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2409.42 seconds
wall clock time: 46 minutes 40.40 seconds (2800.40 seconds total)