Starting phenix.real_space_refine
on Fri Nov 15 13:31:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/11_2024/8exp_28658.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/11_2024/8exp_28658.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/8exp_28658/11_2024/8exp_28658.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/11_2024/8exp_28658.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/11_2024/8exp_28658.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/11_2024/8exp_28658.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=   0.003 sd=   0.039
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
     Zn      2      6.06       5
     S      38      5.16       5
     C    5928      2.51       5
     N    1484      2.21       5
     O    1572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 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: 9024
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4511
          Classifications: {'peptide': 539}
          Link IDs: {'PTRANS': 10, 'TRANS': 528}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.41, per 1000 atoms: 0.93
  Number of scatterers: 9024
  At special positions: 0
  Unit cell: (73.9927, 106.477, 135.353, 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)
     Zn      2     29.99
     S      38     16.00
     O    1572      8.00
     N    1484      7.00
     C    5928      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: 2.74
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "


  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      56.6% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 31
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 46
    Processing helix  chain 'A' and resid 99 through 133
      removed outlier: 3.514A  pdb=" N   LYS A 133 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 151
    Processing helix  chain 'A' and resid 184 through 189
    Processing helix  chain 'A' and resid 194 through 208
      removed outlier: 3.611A  pdb=" N   ASN A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 224
      removed outlier: 4.058A  pdb=" N   ILE A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 252
      removed outlier: 3.890A  pdb=" N   ILE A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS A 239 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 5.479A  pdb=" N   ASN A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 256'
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.798A  pdb=" N   SER A 268 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 308 through 327
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 387 through 390
    Processing helix  chain 'A' and resid 391 through 402
    Processing helix  chain 'A' and resid 429 through 436
    Processing helix  chain 'A' and resid 438 through 448
      removed outlier: 3.660A  pdb=" N   PHE A 442 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 461
    Processing helix  chain 'A' and resid 484 through 497
    Processing helix  chain 'A' and resid 502 through 513
    Processing helix  chain 'A' and resid 564 through 579
    Processing helix  chain 'B' and resid 2 through 31
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 46
    Processing helix  chain 'B' and resid 99 through 133
      removed outlier: 3.515A  pdb=" N   LYS B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 194 through 208
      removed outlier: 3.611A  pdb=" N   ASN B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 4.058A  pdb=" N   ILE B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 252
      removed outlier: 3.890A  pdb=" N   ILE B 238 " --> pdb=" O   LYS B 234 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN B 252 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 256
      removed outlier: 5.479A  pdb=" N   ASN B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 253 through 256'
    Processing helix  chain 'B' and resid 257 through 268
      removed outlier: 3.798A  pdb=" N   SER B 268 " --> pdb=" O   SER B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 308 through 327
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 352 through 357
    Processing helix  chain 'B' and resid 379 through 382
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 391 through 402
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 438 through 448
      removed outlier: 3.660A  pdb=" N   PHE B 442 " --> pdb=" O   VAL B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 461
    Processing helix  chain 'B' and resid 484 through 497
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.440A  pdb=" N   GLU B 522 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   VAL B 545 " --> pdb=" O   GLU B 522 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   TYR B 524 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY B 543 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LYS B 526 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE B 541 " --> pdb=" O   LYS B 526 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY B 528 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY B 539 " --> pdb=" O   GLY B 528 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLY B 530 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS B 372 " --> pdb=" O   SER B 367 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.967A  pdb=" N   TYR B 521 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LYS B 517 " --> pdb=" O   TYR B 521 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU B 523 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137
      removed outlier: 6.638A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.820A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 372 " --> pdb=" O   SER A 367 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   VAL A 545 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU A 522 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   TYR A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   LYS A 517 " --> pdb=" O   TYR A 521 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.820A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 372 " --> pdb=" O   SER A 367 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   VAL A 545 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU A 522 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 9.576A  pdb=" N   PHE B  90 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   THR A 527 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 8.958A  pdb=" N   THR B  92 " --> pdb=" O   THR A 527 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   THR A 529 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   ILE B  94 " --> pdb=" O   THR A 529 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE A 531 " --> pdb=" O   ILE B  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 385
    Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 137
      removed outlier: 6.638A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ARG B 162 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 384 through 385

    508 hydrogen bonds defined for protein.
    1443 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: 2.79

  Time building geometry restraints manager: 3.06 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1597
        1.31 -     1.44: 2750
        1.44 -     1.57: 4765
        1.57 -     1.70: 50
        1.70 -     1.83: 70
  Bond restraints: 9232
  Sorted by residual:
  bond pdb=" CG  GLN B 487 "
       pdb=" CD  GLN B 487 "
    ideal  model  delta    sigma   weight residual
    1.516  1.379  0.137 2.50e-02 1.60e+03 3.02e+01
  bond pdb=" CG  GLN A 487 "
       pdb=" CD  GLN A 487 "
    ideal  model  delta    sigma   weight residual
    1.516  1.379  0.137 2.50e-02 1.60e+03 2.99e+01
  bond pdb=" CB  TYR A 552 "
       pdb=" CG  TYR A 552 "
    ideal  model  delta    sigma   weight residual
    1.512  1.393  0.119 2.20e-02 2.07e+03 2.91e+01
  bond pdb=" CB  TYR B 552 "
       pdb=" CG  TYR B 552 "
    ideal  model  delta    sigma   weight residual
    1.512  1.394  0.118 2.20e-02 2.07e+03 2.89e+01
  bond pdb=" CB  TYR B 521 "
       pdb=" CG  TYR B 521 "
    ideal  model  delta    sigma   weight residual
    1.512  1.407  0.105 2.20e-02 2.07e+03 2.29e+01
  ... (remaining 9227 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 10423
        2.21 -     4.41: 1685
        4.41 -     6.62: 232
        6.62 -     8.82: 66
        8.82 -    11.03: 16
  Bond angle restraints: 12422
  Sorted by residual:
  angle pdb=" N   ILE B 404 "
        pdb=" CA  ILE B 404 "
        pdb=" C   ILE B 404 "
      ideal   model   delta    sigma   weight residual
     110.82  102.10    8.72 9.70e-01 1.06e+00 8.08e+01
  angle pdb=" N   ILE A 404 "
        pdb=" CA  ILE A 404 "
        pdb=" C   ILE A 404 "
      ideal   model   delta    sigma   weight residual
     110.82  102.11    8.71 9.70e-01 1.06e+00 8.07e+01
  angle pdb=" CA  PHE B 313 "
        pdb=" CB  PHE B 313 "
        pdb=" CG  PHE B 313 "
      ideal   model   delta    sigma   weight residual
     113.80  105.01    8.79 1.00e+00 1.00e+00 7.73e+01
  angle pdb=" CA  PHE A 313 "
        pdb=" CB  PHE A 313 "
        pdb=" CG  PHE A 313 "
      ideal   model   delta    sigma   weight residual
     113.80  105.03    8.77 1.00e+00 1.00e+00 7.69e+01
  angle pdb=" CA  LYS B 354 "
        pdb=" C   LYS B 354 "
        pdb=" N   ILE B 355 "
      ideal   model   delta    sigma   weight residual
     118.41  107.38   11.03 1.34e+00 5.57e-01 6.77e+01
  ... (remaining 12417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.75: 5230
       15.75 -    31.50: 226
       31.50 -    47.25: 42
       47.25 -    63.01: 30
       63.01 -    78.76: 6
  Dihedral angle restraints: 5534
    sinusoidal: 2308
      harmonic: 3226
  Sorted by residual:
  dihedral pdb=" C   ASN A 302 "
           pdb=" N   ASN A 302 "
           pdb=" CA  ASN A 302 "
           pdb=" CB  ASN A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.90   -7.70     0      2.50e+00 1.60e-01 9.48e+00
  dihedral pdb=" C   ASN B 302 "
           pdb=" N   ASN B 302 "
           pdb=" CA  ASN B 302 "
           pdb=" CB  ASN B 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.92   -7.68     0      2.50e+00 1.60e-01 9.43e+00
  dihedral pdb=" CG  LYS B 352 "
           pdb=" CD  LYS B 352 "
           pdb=" CE  LYS B 352 "
           pdb=" NZ  LYS B 352 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  127.15   52.85     3      1.50e+01 4.44e-03 9.15e+00
  ... (remaining 5531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 742
       0.075 -    0.149: 443
       0.149 -    0.224: 143
       0.224 -    0.299: 23
       0.299 -    0.374: 7
  Chirality restraints: 1358
  Sorted by residual:
  chirality pdb=" CA  PHE A 313 "
            pdb=" N   PHE A 313 "
            pdb=" C   PHE A 313 "
            pdb=" CB  PHE A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.49e+00
  chirality pdb=" CA  PHE B 313 "
            pdb=" N   PHE B 313 "
            pdb=" C   PHE B 313 "
            pdb=" CB  PHE B 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CG  LEU B 400 "
            pdb=" CB  LEU B 400 "
            pdb=" CD1 LEU B 400 "
            pdb=" CD2 LEU B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.92    0.33 2.00e-01 2.50e+01 2.73e+00
  ... (remaining 1355 not shown)

  Planarity restraints: 1520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 463 "   -0.064 2.00e-02 2.50e+03   3.41e-02 2.33e+01
        pdb=" CG  TYR A 463 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 463 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 463 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 463 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 463 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 463 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 463 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 463 "    0.064 2.00e-02 2.50e+03   3.41e-02 2.33e+01
        pdb=" CG  TYR B 463 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 463 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 463 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 463 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 463 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 463 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 463 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 540 "   -0.062 2.00e-02 2.50e+03   3.01e-02 2.26e+01
        pdb=" CG  TRP B 540 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 540 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 540 "    0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 540 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 540 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 540 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 540 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 540 "    0.019 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 540 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1517 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 93
        2.60 -     3.18: 8700
        3.18 -     3.75: 14641
        3.75 -     4.33: 21209
        4.33 -     4.90: 32042
  Nonbonded interactions: 76685
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.031 2.230
  nonbonded pdb=" OE1 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.031 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.039 2.230
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.040 2.230
  nonbonded pdb=" CE  MET A 266 "
            pdb=" CE  MET B 266 "
     model   vdw
     2.109 3.880
  ... (remaining 76680 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:             0.080
  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:          0.290
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     28.990
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4467
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      :  0.019   0.137   9232  Z= 1.212
  Angle     :  1.741  11.026  12422  Z= 1.196
  Chirality :  0.099   0.374   1358
  Planarity :  0.008   0.037   1520
  Dihedral  : 10.687  78.757   3454
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.38 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.39 %
    Favored  : 98.02 %
  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: -0.04 (0.24), residues: 1066
  helix:  0.31 (0.19), residues: 564
  sheet:  0.61 (0.44), residues: 138
  loop : -0.63 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.008   TRP B 540 
 HIS   0.008   0.003   HIS A 549 
 PHE   0.031   0.007   PHE B 313 
 TYR   0.064   0.009   TYR A 463 
 ARG   0.006   0.001   ARG B 235 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 295
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.8887 (mt) cc_final: 0.8678 (mp)
REVERT: A   19 LEU cc_start: 0.9464 (mt) cc_final: 0.9164 (mt)
REVERT: A  103 ASP cc_start: 0.8144 (m-30) cc_final: 0.7872 (m-30)
REVERT: A  127 TYR cc_start: 0.8533 (t80) cc_final: 0.7905 (t80)
REVERT: A  143 LYS cc_start: 0.8616 (tttt) cc_final: 0.8193 (tttp)
REVERT: A  220 PHE cc_start: 0.7908 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  224 MET cc_start: 0.8780 (mpp) cc_final: 0.8216 (mpp)
REVERT: A  263 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7900 (mt-10)
REVERT: A  265 ILE cc_start: 0.9198 (mm) cc_final: 0.8990 (mm)
REVERT: A  300 GLU cc_start: 0.7976 (tp30) cc_final: 0.7646 (tp30)
REVERT: A  316 ILE cc_start: 0.8464 (mt) cc_final: 0.8232 (mm)
REVERT: A  317 PHE cc_start: 0.8448 (m-80) cc_final: 0.8063 (m-10)
REVERT: A  322 MET cc_start: 0.8742 (mtm) cc_final: 0.8485 (mtm)
REVERT: A  404 ILE cc_start: 0.5036 (mt) cc_final: 0.4045 (mm)
REVERT: B   19 LEU cc_start: 0.9478 (mt) cc_final: 0.9109 (mt)
REVERT: B  127 TYR cc_start: 0.8418 (t80) cc_final: 0.7708 (t80)
REVERT: B  143 LYS cc_start: 0.8450 (tttt) cc_final: 0.8065 (tttp)
REVERT: B  180 ILE cc_start: 0.8138 (mt) cc_final: 0.7836 (mm)
REVERT: B  220 PHE cc_start: 0.7891 (m-80) cc_final: 0.7539 (m-80)
REVERT: B  224 MET cc_start: 0.8768 (mpp) cc_final: 0.8285 (mpp)
REVERT: B  227 ASN cc_start: 0.8067 (t0) cc_final: 0.7865 (t0)
REVERT: B  300 GLU cc_start: 0.7970 (tp30) cc_final: 0.7383 (tm-30)
REVERT: B  316 ILE cc_start: 0.8487 (mt) cc_final: 0.8287 (mm)
REVERT: B  317 PHE cc_start: 0.8426 (m-80) cc_final: 0.8161 (m-10)
REVERT: B  321 LEU cc_start: 0.8761 (mt) cc_final: 0.8551 (mt)
REVERT: B  404 ILE cc_start: 0.5004 (mt) cc_final: 0.4113 (mm)
  outliers start: 6
  outliers final: 1
  residues processed: 301
  average time/residue: 0.2800
  time to fit residues: 109.6745
Evaluate side-chains
  184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 153 HIS
** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 457 GLN
A 557 HIS
B 134 GLN
B 153 HIS
** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 457 GLN
B 557 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4692
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9232  Z= 0.360
  Angle     :  0.776   8.398  12422  Z= 0.430
  Chirality :  0.050   0.191   1358
  Planarity :  0.005   0.045   1520
  Dihedral  :  5.523  22.255   1174
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.98 %
    Favored  : 96.92 %
  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: -0.06 (0.25), residues: 1066
  helix:  0.51 (0.21), residues: 564
  sheet:  0.75 (0.47), residues: 124
  loop : -1.06 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 174 
 HIS   0.008   0.002   HIS A 205 
 PHE   0.021   0.003   PHE B  21 
 TYR   0.029   0.003   TYR A 394 
 ARG   0.005   0.001   ARG A 384 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.9464 (mt) cc_final: 0.9150 (mt)
REVERT: A  143 LYS cc_start: 0.8798 (tttt) cc_final: 0.8322 (tttp)
REVERT: A  224 MET cc_start: 0.8154 (mpp) cc_final: 0.7842 (mmm)
REVERT: A  300 GLU cc_start: 0.9096 (tp30) cc_final: 0.8184 (tm-30)
REVERT: A  321 LEU cc_start: 0.9068 (mt) cc_final: 0.8627 (mt)
REVERT: B   12 PHE cc_start: 0.8761 (t80) cc_final: 0.8257 (t80)
REVERT: B   19 LEU cc_start: 0.9450 (mt) cc_final: 0.9192 (mt)
REVERT: B   33 MET cc_start: 0.7736 (mmp) cc_final: 0.7518 (mmp)
REVERT: B   96 LYS cc_start: 0.5585 (tptt) cc_final: 0.5353 (tmtt)
REVERT: B  113 LEU cc_start: 0.8418 (mt) cc_final: 0.8190 (mt)
REVERT: B  137 TYR cc_start: 0.7402 (p90) cc_final: 0.7149 (p90)
REVERT: B  143 LYS cc_start: 0.8767 (tttt) cc_final: 0.8388 (tttp)
REVERT: B  224 MET cc_start: 0.8154 (mpp) cc_final: 0.7853 (mmm)
REVERT: B  227 ASN cc_start: 0.7691 (t0) cc_final: 0.7405 (t0)
REVERT: B  265 ILE cc_start: 0.9012 (mp) cc_final: 0.8681 (mp)
REVERT: B  300 GLU cc_start: 0.8983 (tp30) cc_final: 0.7977 (tm-30)
REVERT: B  321 LEU cc_start: 0.9104 (mt) cc_final: 0.8748 (mt)
REVERT: B  495 MET cc_start: 0.5372 (mtt) cc_final: 0.4996 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2438
  time to fit residues: 71.3540
Evaluate side-chains
  172 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0970
   chunk 80 optimal weight:    0.0980
   chunk 65 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 96 optimal weight:   30.0000
   chunk 104 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 32 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
B 302 ASN
B 537 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4553
moved from start:          0.4974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9232  Z= 0.180
  Angle     :  0.588   6.457  12422  Z= 0.326
  Chirality :  0.045   0.184   1358
  Planarity :  0.003   0.037   1520
  Dihedral  :  4.927  19.502   1174
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.88 %
    Favored  : 97.02 %
  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:  0.52 (0.26), residues: 1066
  helix:  1.05 (0.21), residues: 566
  sheet:  0.47 (0.44), residues: 138
  loop : -0.73 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 110 
 HIS   0.003   0.001   HIS B 282 
 PHE   0.040   0.002   PHE A  14 
 TYR   0.012   0.002   TYR B 175 
 ARG   0.004   0.000   ARG B 293 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.8534 (tp) cc_final: 0.8287 (tp)
REVERT: A   19 LEU cc_start: 0.9460 (mt) cc_final: 0.9068 (mt)
REVERT: A  126 LEU cc_start: 0.8870 (mt) cc_final: 0.8595 (mt)
REVERT: A  137 TYR cc_start: 0.6674 (p90) cc_final: 0.6234 (p90)
REVERT: A  143 LYS cc_start: 0.8826 (tttt) cc_final: 0.8485 (tptt)
REVERT: A  150 LEU cc_start: 0.8540 (tp) cc_final: 0.8319 (tp)
REVERT: A  180 ILE cc_start: 0.7958 (mt) cc_final: 0.7652 (mm)
REVERT: A  224 MET cc_start: 0.8418 (mpp) cc_final: 0.7979 (mmm)
REVERT: A  233 VAL cc_start: 0.8171 (t) cc_final: 0.7865 (p)
REVERT: A  265 ILE cc_start: 0.8897 (mm) cc_final: 0.8685 (mm)
REVERT: A  300 GLU cc_start: 0.9017 (tp30) cc_final: 0.7944 (tm-30)
REVERT: A  321 LEU cc_start: 0.9161 (mt) cc_final: 0.8656 (mt)
REVERT: A  394 TYR cc_start: 0.5354 (m-80) cc_final: 0.4852 (m-80)
REVERT: B    5 LEU cc_start: 0.8552 (tp) cc_final: 0.8319 (tp)
REVERT: B   12 PHE cc_start: 0.8729 (t80) cc_final: 0.8288 (t80)
REVERT: B   33 MET cc_start: 0.8162 (mmp) cc_final: 0.7753 (mmp)
REVERT: B   95 HIS cc_start: 0.3592 (t70) cc_final: 0.3309 (t70)
REVERT: B  126 LEU cc_start: 0.8830 (mt) cc_final: 0.8517 (mt)
REVERT: B  143 LYS cc_start: 0.8622 (tttt) cc_final: 0.8168 (tttp)
REVERT: B  224 MET cc_start: 0.8446 (mpp) cc_final: 0.7972 (mmm)
REVERT: B  227 ASN cc_start: 0.8062 (t0) cc_final: 0.7860 (t0)
REVERT: B  233 VAL cc_start: 0.8196 (t) cc_final: 0.7810 (p)
REVERT: B  265 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8648 (mp)
REVERT: B  300 GLU cc_start: 0.8989 (tp30) cc_final: 0.7958 (tm-30)
REVERT: B  321 LEU cc_start: 0.9076 (mt) cc_final: 0.8784 (mt)
REVERT: B  365 MET cc_start: -0.0959 (tpt) cc_final: -0.3424 (mmm)
REVERT: B  495 MET cc_start: 0.5083 (mtt) cc_final: 0.4542 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2297
  time to fit residues: 70.4653
Evaluate side-chains
  177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 72 optimal weight:    0.0170
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 96 optimal weight:   30.0000
   chunk 102 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 85 optimal weight:   20.0000
   overall best weight:    1.9022

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 484 ASN
B 144 ASN
B 484 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4621
moved from start:          0.5632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9232  Z= 0.223
  Angle     :  0.611   8.300  12422  Z= 0.337
  Chirality :  0.044   0.166   1358
  Planarity :  0.004   0.036   1520
  Dihedral  :  4.876  20.273   1174
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.88 %
    Favored  : 97.02 %
  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:  0.37 (0.26), residues: 1066
  helix:  1.01 (0.21), residues: 582
  sheet:  0.60 (0.47), residues: 132
  loop : -1.13 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 205 
 PHE   0.035   0.002   PHE B  14 
 TYR   0.027   0.002   TYR A 394 
 ARG   0.003   0.000   ARG A 194 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 TYR cc_start: 0.6928 (p90) cc_final: 0.6631 (p90)
REVERT: A  143 LYS cc_start: 0.8828 (tttt) cc_final: 0.8403 (tptt)
REVERT: A  224 MET cc_start: 0.8450 (mpp) cc_final: 0.8018 (mmm)
REVERT: A  233 VAL cc_start: 0.7999 (t) cc_final: 0.7619 (p)
REVERT: A  265 ILE cc_start: 0.8830 (mm) cc_final: 0.8614 (mm)
REVERT: A  300 GLU cc_start: 0.9134 (tp30) cc_final: 0.8222 (tm-30)
REVERT: A  321 LEU cc_start: 0.9156 (mt) cc_final: 0.8860 (mt)
REVERT: B  126 LEU cc_start: 0.8893 (mt) cc_final: 0.8677 (mt)
REVERT: B  138 LEU cc_start: 0.6541 (tp) cc_final: 0.6241 (tp)
REVERT: B  143 LYS cc_start: 0.8630 (tttt) cc_final: 0.8150 (tttp)
REVERT: B  224 MET cc_start: 0.8487 (mpp) cc_final: 0.8005 (mmm)
REVERT: B  233 VAL cc_start: 0.7946 (t) cc_final: 0.7600 (p)
REVERT: B  300 GLU cc_start: 0.9171 (tp30) cc_final: 0.8341 (tm-30)
REVERT: B  321 LEU cc_start: 0.9125 (mt) cc_final: 0.8784 (mt)
REVERT: B  365 MET cc_start: -0.2446 (tpt) cc_final: -0.4464 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 203
  average time/residue: 0.2286
  time to fit residues: 63.4939
Evaluate side-chains
  175 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 174
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:   30.0000
   chunk 87 optimal weight:   30.0000
   chunk 70 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 91 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 34 optimal weight:   20.0000
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN
A 285 ASN
B 158 ASN
B 285 ASN
B 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4865
moved from start:          0.6375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   9232  Z= 0.401
  Angle     :  0.806  10.526  12422  Z= 0.440
  Chirality :  0.049   0.172   1358
  Planarity :  0.005   0.054   1520
  Dihedral  :  5.604  23.735   1174
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 19.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.40 (0.25), residues: 1066
  helix:  0.44 (0.20), residues: 584
  sheet:  0.32 (0.49), residues: 124
  loop : -1.57 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP A 110 
 HIS   0.009   0.002   HIS B 549 
 PHE   0.036   0.003   PHE B  14 
 TYR   0.020   0.003   TYR B 178 
 ARG   0.006   0.001   ARG B 162 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8097 (t80) cc_final: 0.7798 (t80)
REVERT: A   15 ILE cc_start: 0.9216 (mm) cc_final: 0.8398 (mm)
REVERT: A  143 LYS cc_start: 0.9032 (tttt) cc_final: 0.8707 (tttp)
REVERT: A  227 ASN cc_start: 0.7889 (t0) cc_final: 0.7623 (t0)
REVERT: A  265 ILE cc_start: 0.9002 (mm) cc_final: 0.8784 (mm)
REVERT: A  321 LEU cc_start: 0.9182 (mt) cc_final: 0.8729 (mt)
REVERT: A  394 TYR cc_start: 0.4321 (m-80) cc_final: 0.3923 (m-80)
REVERT: B   19 LEU cc_start: 0.9446 (tp) cc_final: 0.9220 (tp)
REVERT: B  138 LEU cc_start: 0.7509 (tp) cc_final: 0.7175 (tt)
REVERT: B  143 LYS cc_start: 0.8930 (tttt) cc_final: 0.8624 (tttp)
REVERT: B  227 ASN cc_start: 0.7977 (t0) cc_final: 0.7727 (t0)
REVERT: B  321 LEU cc_start: 0.9278 (mt) cc_final: 0.9022 (mt)
REVERT: B  365 MET cc_start: -0.2226 (tpt) cc_final: -0.4034 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2075
  time to fit residues: 55.4560
Evaluate side-chains
  156 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 102 optimal weight:   20.0000
   chunk 85 optimal weight:   30.0000
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4758
moved from start:          0.6682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9232  Z= 0.251
  Angle     :  0.651   7.034  12422  Z= 0.355
  Chirality :  0.045   0.177   1358
  Planarity :  0.004   0.035   1520
  Dihedral  :  5.324  22.724   1174
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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: -0.03 (0.26), residues: 1066
  helix:  0.82 (0.21), residues: 584
  sheet:  0.60 (0.53), residues: 110
  loop : -1.53 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  99 
 HIS   0.005   0.001   HIS A 205 
 PHE   0.022   0.002   PHE B  12 
 TYR   0.026   0.002   TYR B 373 
 ARG   0.004   0.001   ARG B 162 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8171 (t80) cc_final: 0.7909 (t80)
REVERT: A   15 ILE cc_start: 0.9134 (mm) cc_final: 0.8735 (mm)
REVERT: A  126 LEU cc_start: 0.8647 (mm) cc_final: 0.8037 (mm)
REVERT: A  143 LYS cc_start: 0.9128 (tttt) cc_final: 0.8830 (tttp)
REVERT: A  224 MET cc_start: 0.8215 (mtp) cc_final: 0.6830 (tpp)
REVERT: A  227 ASN cc_start: 0.7815 (t0) cc_final: 0.7579 (t0)
REVERT: A  265 ILE cc_start: 0.8971 (mm) cc_final: 0.8749 (mm)
REVERT: A  321 LEU cc_start: 0.9350 (mt) cc_final: 0.8967 (mt)
REVERT: A  365 MET cc_start: -0.3131 (tpt) cc_final: -0.4000 (tpt)
REVERT: A  394 TYR cc_start: 0.4586 (m-80) cc_final: 0.4377 (m-80)
REVERT: B    1 MET cc_start: 0.4906 (ttt) cc_final: 0.4581 (tpp)
REVERT: B   15 ILE cc_start: 0.9138 (mm) cc_final: 0.8748 (mm)
REVERT: B  126 LEU cc_start: 0.8910 (mt) cc_final: 0.8688 (mt)
REVERT: B  143 LYS cc_start: 0.8973 (tttt) cc_final: 0.8673 (tttp)
REVERT: B  224 MET cc_start: 0.8258 (mtp) cc_final: 0.6813 (tpp)
REVERT: B  227 ASN cc_start: 0.7257 (t0) cc_final: 0.6872 (t0)
REVERT: B  293 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7271 (mtm-85)
REVERT: B  321 LEU cc_start: 0.9309 (mt) cc_final: 0.9023 (mt)
REVERT: B  365 MET cc_start: -0.2388 (tpt) cc_final: -0.4179 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2143
  time to fit residues: 56.7601
Evaluate side-chains
  160 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 102 optimal weight:   20.0000
   chunk 63 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0980
   chunk 40 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4640
moved from start:          0.6971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9232  Z= 0.175
  Angle     :  0.608   8.029  12422  Z= 0.325
  Chirality :  0.044   0.178   1358
  Planarity :  0.003   0.039   1520
  Dihedral  :  4.932  20.659   1174
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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:  0.25 (0.26), residues: 1066
  helix:  1.12 (0.21), residues: 584
  sheet:  0.47 (0.51), residues: 114
  loop : -1.47 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 110 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.019   0.001   PHE B 121 
 TYR   0.022   0.001   TYR A 337 
 ARG   0.007   0.000   ARG B 247 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8117 (t80) cc_final: 0.7809 (t80)
REVERT: A   15 ILE cc_start: 0.9031 (mm) cc_final: 0.8618 (mm)
REVERT: A  123 LYS cc_start: 0.7422 (ttpt) cc_final: 0.7135 (ptmm)
REVERT: A  126 LEU cc_start: 0.8722 (mm) cc_final: 0.8338 (mm)
REVERT: A  143 LYS cc_start: 0.8950 (tttt) cc_final: 0.8573 (tptt)
REVERT: A  217 PHE cc_start: 0.8963 (t80) cc_final: 0.8337 (t80)
REVERT: A  227 ASN cc_start: 0.7651 (t0) cc_final: 0.7362 (t0)
REVERT: A  233 VAL cc_start: 0.8235 (t) cc_final: 0.7830 (p)
REVERT: A  265 ILE cc_start: 0.8859 (mm) cc_final: 0.8635 (mm)
REVERT: A  321 LEU cc_start: 0.9314 (mt) cc_final: 0.8971 (mt)
REVERT: A  365 MET cc_start: -0.3383 (tpt) cc_final: -0.4126 (tpt)
REVERT: B   15 ILE cc_start: 0.9108 (mm) cc_final: 0.8809 (mm)
REVERT: B  143 LYS cc_start: 0.9057 (tttt) cc_final: 0.8625 (tttp)
REVERT: B  227 ASN cc_start: 0.6821 (t0) cc_final: 0.6360 (t0)
REVERT: B  321 LEU cc_start: 0.9277 (mt) cc_final: 0.8960 (mt)
REVERT: B  342 PRO cc_start: 0.3314 (Cg_exo) cc_final: 0.2867 (Cg_endo)
REVERT: B  365 MET cc_start: -0.2481 (tpt) cc_final: -0.4348 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2191
  time to fit residues: 59.3438
Evaluate side-chains
  161 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 92 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4665
moved from start:          0.7269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9232  Z= 0.198
  Angle     :  0.637  13.215  12422  Z= 0.340
  Chirality :  0.045   0.267   1358
  Planarity :  0.003   0.032   1520
  Dihedral  :  4.880  19.070   1174
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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 (0.26), residues: 1066
  helix:  1.15 (0.22), residues: 586
  sheet:  0.55 (0.52), residues: 114
  loop : -1.46 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 110 
 HIS   0.005   0.001   HIS B 201 
 PHE   0.022   0.002   PHE B 121 
 TYR   0.023   0.002   TYR B 373 
 ARG   0.005   0.000   ARG B 247 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8029 (t80) cc_final: 0.7724 (t80)
REVERT: A   15 ILE cc_start: 0.9038 (mm) cc_final: 0.8713 (mm)
REVERT: A  123 LYS cc_start: 0.7439 (ttpt) cc_final: 0.7100 (ptmm)
REVERT: A  126 LEU cc_start: 0.8888 (mm) cc_final: 0.8633 (mm)
REVERT: A  143 LYS cc_start: 0.8961 (tttt) cc_final: 0.8602 (tptt)
REVERT: A  173 PHE cc_start: 0.7449 (t80) cc_final: 0.6943 (t80)
REVERT: A  217 PHE cc_start: 0.8985 (t80) cc_final: 0.8424 (t80)
REVERT: A  227 ASN cc_start: 0.7801 (t0) cc_final: 0.7461 (t0)
REVERT: A  317 PHE cc_start: 0.7949 (m-10) cc_final: 0.7742 (m-10)
REVERT: A  321 LEU cc_start: 0.9371 (mt) cc_final: 0.9091 (mt)
REVERT: A  365 MET cc_start: -0.3502 (tpt) cc_final: -0.4185 (tpt)
REVERT: B    1 MET cc_start: 0.5455 (mmm) cc_final: 0.5191 (mmt)
REVERT: B   15 ILE cc_start: 0.9131 (mm) cc_final: 0.8781 (mm)
REVERT: B   96 LYS cc_start: 0.4354 (tptt) cc_final: 0.3093 (tmtt)
REVERT: B  126 LEU cc_start: 0.8803 (mm) cc_final: 0.8464 (mm)
REVERT: B  143 LYS cc_start: 0.8867 (tttt) cc_final: 0.8440 (tttp)
REVERT: B  173 PHE cc_start: 0.7208 (t80) cc_final: 0.6458 (t80)
REVERT: B  227 ASN cc_start: 0.6797 (t0) cc_final: 0.6363 (t0)
REVERT: B  321 LEU cc_start: 0.9327 (mt) cc_final: 0.9016 (mt)
REVERT: B  365 MET cc_start: -0.2605 (tpt) cc_final: -0.4336 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.2179
  time to fit residues: 56.9909
Evaluate side-chains
  163 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 97 optimal weight:   20.0000
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:   20.0000
   chunk 74 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 86 optimal weight:   30.0000
   chunk 90 optimal weight:    9.9990
   chunk 94 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 100 optimal weight:    0.4980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B 278 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4665
moved from start:          0.7508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9232  Z= 0.195
  Angle     :  0.652   9.400  12422  Z= 0.343
  Chirality :  0.045   0.263   1358
  Planarity :  0.003   0.036   1520
  Dihedral  :  4.796  16.951   1174
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.30 %
    Favored  : 99.60 %
  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:  0.22 (0.26), residues: 1066
  helix:  1.12 (0.22), residues: 586
  sheet:  0.41 (0.52), residues: 114
  loop : -1.54 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 110 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.020   0.002   PHE B 121 
 TYR   0.015   0.001   TYR B 366 
 ARG   0.005   0.000   ARG B 247 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9044 (mm) cc_final: 0.8743 (mm)
REVERT: A  123 LYS cc_start: 0.7470 (ttpt) cc_final: 0.7103 (ptmm)
REVERT: A  143 LYS cc_start: 0.9062 (tttt) cc_final: 0.8673 (tptt)
REVERT: A  217 PHE cc_start: 0.9044 (t80) cc_final: 0.8403 (t80)
REVERT: A  224 MET cc_start: 0.8169 (mtp) cc_final: 0.6779 (tpp)
REVERT: A  227 ASN cc_start: 0.7806 (t0) cc_final: 0.7584 (t0)
REVERT: A  265 ILE cc_start: 0.8454 (mm) cc_final: 0.8210 (mm)
REVERT: A  321 LEU cc_start: 0.9391 (mt) cc_final: 0.9036 (mt)
REVERT: A  365 MET cc_start: -0.3714 (tpt) cc_final: -0.4270 (tpt)
REVERT: B    5 LEU cc_start: 0.8379 (tp) cc_final: 0.8156 (tp)
REVERT: B  123 LYS cc_start: 0.7739 (ttpt) cc_final: 0.6936 (ptmm)
REVERT: B  143 LYS cc_start: 0.8799 (tttt) cc_final: 0.8377 (tttp)
REVERT: B  213 HIS cc_start: 0.7730 (m90) cc_final: 0.7505 (m90)
REVERT: B  224 MET cc_start: 0.7956 (mtp) cc_final: 0.6421 (tpp)
REVERT: B  227 ASN cc_start: 0.6955 (t0) cc_final: 0.6557 (t0)
REVERT: B  233 VAL cc_start: 0.8059 (t) cc_final: 0.7686 (p)
REVERT: B  321 LEU cc_start: 0.9308 (mt) cc_final: 0.9009 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 187
  average time/residue: 0.2235
  time to fit residues: 57.9701
Evaluate side-chains
  167 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0870
   chunk 105 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 64 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    0.8562

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

Flipped N/Q/H residues before XYZ refinement:
B 278 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4611
moved from start:          0.7692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9232  Z= 0.183
  Angle     :  0.659  14.233  12422  Z= 0.347
  Chirality :  0.045   0.223   1358
  Planarity :  0.003   0.030   1520
  Dihedral  :  4.758  16.553   1174
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.30 %
    Favored  : 99.60 %
  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:  0.22 (0.26), residues: 1066
  helix:  1.15 (0.22), residues: 586
  sheet:  0.31 (0.52), residues: 114
  loop : -1.55 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 110 
 HIS   0.005   0.001   HIS B 201 
 PHE   0.020   0.001   PHE B 491 
 TYR   0.020   0.001   TYR B 373 
 ARG   0.003   0.000   ARG A 162 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4930 (tpp) cc_final: 0.4539 (mmt)
REVERT: A   12 PHE cc_start: 0.7968 (t80) cc_final: 0.7650 (t80)
REVERT: A   15 ILE cc_start: 0.9011 (mm) cc_final: 0.8809 (mm)
REVERT: A   36 TYR cc_start: 0.7674 (p90) cc_final: 0.7445 (p90)
REVERT: A  143 LYS cc_start: 0.8994 (tttt) cc_final: 0.8663 (tptt)
REVERT: A  224 MET cc_start: 0.7754 (mtp) cc_final: 0.6513 (tpp)
REVERT: A  227 ASN cc_start: 0.7738 (t0) cc_final: 0.7472 (t0)
REVERT: A  265 ILE cc_start: 0.8554 (mm) cc_final: 0.8352 (mm)
REVERT: A  317 PHE cc_start: 0.8145 (m-10) cc_final: 0.7834 (m-10)
REVERT: A  321 LEU cc_start: 0.9357 (mt) cc_final: 0.9024 (mt)
REVERT: A  365 MET cc_start: -0.3852 (tpt) cc_final: -0.4330 (tpt)
REVERT: B    5 LEU cc_start: 0.8438 (tp) cc_final: 0.8218 (tp)
REVERT: B  129 LYS cc_start: 0.8023 (pttm) cc_final: 0.7641 (tmmt)
REVERT: B  143 LYS cc_start: 0.8798 (tttt) cc_final: 0.8296 (tttp)
REVERT: B  213 HIS cc_start: 0.7886 (m90) cc_final: 0.7578 (m90)
REVERT: B  227 ASN cc_start: 0.6784 (t0) cc_final: 0.6391 (t0)
REVERT: B  259 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8340 (mmmm)
REVERT: B  321 LEU cc_start: 0.9294 (mt) cc_final: 0.9007 (mt)
REVERT: B  494 MET cc_start: 0.6106 (ptm) cc_final: 0.5870 (ptm)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2060
  time to fit residues: 56.2489
Evaluate side-chains
  168 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 12 optimal weight:    0.3980
   chunk 23 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 86 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0070
   chunk 73 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
B 278 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.208764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.142619 restraints weight = 22160.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.147695 restraints weight = 13441.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.150949 restraints weight = 9319.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.7909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9232  Z= 0.171
  Angle     :  0.632  10.477  12422  Z= 0.334
  Chirality :  0.044   0.197   1358
  Planarity :  0.003   0.036   1520
  Dihedral  :  4.540  15.096   1174
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  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:  0.29 (0.26), residues: 1066
  helix:  1.21 (0.22), residues: 586
  sheet:  0.31 (0.53), residues: 114
  loop : -1.53 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 110 
 HIS   0.006   0.001   HIS B 201 
 PHE   0.019   0.001   PHE B 491 
 TYR   0.015   0.001   TYR B 463 
 ARG   0.004   0.000   ARG B 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2077.54 seconds
wall clock time: 38 minutes 51.45 seconds (2331.45 seconds total)