Starting phenix.real_space_refine
on Sat Aug 23 01:33:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exp_28658/08_2025/8exp_28658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exp_28658/08_2025/8exp_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exp_28658/08_2025/8exp_28658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exp_28658/08_2025/8exp_28658.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exp_28658/08_2025/8exp_28658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exp_28658/08_2025/8exp_28658.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.65, per 1000 atoms: 0.29
  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: 0.68
  Conformation dependent library (CDL) restraints added in 435.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 0.33
  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: 1.29

  Time building geometry restraints manager: 0.92 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: 0.01
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:             0.090
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.440
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.670
-------------------------------------------------------------------------------
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   9236  Z= 1.041
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.24), residues: 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
 ARG   0.006   0.001   ARG B 235 
 TYR   0.064   0.009   TYR A 463 
 PHE   0.031   0.007   PHE B 313 
 TRP   0.062   0.008   TRP B 540 
 HIS   0.008   0.003   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.01909 ( 9232)
  covalent geometry    : angle       1.74100 (12422)
  hydrogen bonds       : bond        0.19724 (  481)
  hydrogen bonds       : angle       7.54805 ( 1443)
  metal coordination   : bond        0.04156 (    4)

*********************** 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  : 0.284 
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: 0.0981
  time to fit residues: 39.0756
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  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 302 ASN
A 457 GLN
A 557 HIS
B 134 GLN
B 302 ASN
B 306 GLN
B 537 ASN
B 557 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.206780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.145411 restraints weight = 21104.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.150558 restraints weight = 12407.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.153860 restraints weight = 8448.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.156190 restraints weight = 6349.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.157667 restraints weight = 5115.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9236  Z= 0.177
  Angle     :  0.666   7.217  12422  Z= 0.372
  Chirality :  0.047   0.187   1358
  Planarity :  0.004   0.029   1520
  Dihedral  :  5.175  21.350   1174
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.18 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.25), residues: 1066
  helix:  0.97 (0.21), residues: 566
  sheet:  0.77 (0.45), residues: 138
  loop : -0.74 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 247 
 TYR   0.031   0.002   TYR A 394 
 PHE   0.021   0.002   PHE A 442 
 TRP   0.018   0.002   TRP A 174 
 HIS   0.005   0.001   HIS A 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9232)
  covalent geometry    : angle       0.66599 (12422)
  hydrogen bonds       : bond        0.06893 (  481)
  hydrogen bonds       : angle       5.52540 ( 1443)
  metal coordination   : bond        0.00408 (    4)

*********************** 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
  234 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 232
  time to evaluate  : 0.375 
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    9 ILE cc_start: 0.8752 (mt) cc_final: 0.7732 (mt)
REVERT: A   17 LEU cc_start: 0.9035 (mp) cc_final: 0.8778 (mt)
REVERT: A   19 LEU cc_start: 0.9392 (mt) cc_final: 0.8895 (mt)
REVERT: A  126 LEU cc_start: 0.9245 (mt) cc_final: 0.8893 (mt)
REVERT: A  143 LYS cc_start: 0.8810 (tttt) cc_final: 0.8457 (tptt)
REVERT: A  180 ILE cc_start: 0.7910 (mt) cc_final: 0.7561 (mm)
REVERT: A  211 THR cc_start: 0.8614 (p) cc_final: 0.7917 (t)
REVERT: A  220 PHE cc_start: 0.8630 (m-80) cc_final: 0.8342 (m-10)
REVERT: A  226 TYR cc_start: 0.6424 (p90) cc_final: 0.5491 (p90)
REVERT: A  240 ASP cc_start: 0.8688 (m-30) cc_final: 0.8257 (m-30)
REVERT: A  265 ILE cc_start: 0.8367 (mm) cc_final: 0.8106 (mm)
REVERT: A  300 GLU cc_start: 0.8958 (tp30) cc_final: 0.8005 (tm-30)
REVERT: A  321 LEU cc_start: 0.9237 (mt) cc_final: 0.8924 (mt)
REVERT: A  330 MET cc_start: 0.5840 (ppp) cc_final: 0.5234 (tmm)
REVERT: B    5 LEU cc_start: 0.8718 (mp) cc_final: 0.8219 (tp)
REVERT: B    9 ILE cc_start: 0.8797 (mt) cc_final: 0.8419 (mt)
REVERT: B   12 PHE cc_start: 0.9336 (t80) cc_final: 0.8589 (t80)
REVERT: B   19 LEU cc_start: 0.9321 (mt) cc_final: 0.8854 (mt)
REVERT: B   31 ASN cc_start: 0.8702 (m-40) cc_final: 0.8425 (p0)
REVERT: B  126 LEU cc_start: 0.9189 (mt) cc_final: 0.8871 (mt)
REVERT: B  137 TYR cc_start: 0.7923 (p90) cc_final: 0.7348 (p90)
REVERT: B  143 LYS cc_start: 0.8685 (tttt) cc_final: 0.8124 (tttp)
REVERT: B  180 ILE cc_start: 0.7959 (mt) cc_final: 0.7709 (mm)
REVERT: B  213 HIS cc_start: 0.8218 (m-70) cc_final: 0.7867 (m90)
REVERT: B  220 PHE cc_start: 0.8624 (m-80) cc_final: 0.8338 (m-10)
REVERT: B  226 TYR cc_start: 0.6517 (p90) cc_final: 0.5560 (p90)
REVERT: B  227 ASN cc_start: 0.7840 (t0) cc_final: 0.7414 (t0)
REVERT: B  240 ASP cc_start: 0.8644 (m-30) cc_final: 0.8216 (m-30)
REVERT: B  263 GLU cc_start: 0.8637 (pt0) cc_final: 0.8406 (pp20)
REVERT: B  265 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8126 (mp)
REVERT: B  300 GLU cc_start: 0.8978 (tp30) cc_final: 0.7935 (tm-30)
REVERT: B  321 LEU cc_start: 0.9203 (mt) cc_final: 0.8964 (mt)
REVERT: B  339 TYR cc_start: 0.6889 (t80) cc_final: 0.6502 (t80)
REVERT: B  368 MET cc_start: 0.3397 (mmm) cc_final: 0.3186 (mmm)
REVERT: B  497 GLN cc_start: 0.8425 (mm110) cc_final: 0.7760 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1081
  time to fit residues: 34.0273
Evaluate side-chains
  191 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0020
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0030
   chunk 88 optimal weight:   30.0000
   chunk 54 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
B 457 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.207100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.142478 restraints weight = 21537.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.147708 restraints weight = 12647.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.151088 restraints weight = 8650.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.153257 restraints weight = 6549.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.154860 restraints weight = 5375.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9236  Z= 0.147
  Angle     :  0.605   7.133  12422  Z= 0.330
  Chirality :  0.044   0.188   1358
  Planarity :  0.003   0.034   1520
  Dihedral  :  4.817  18.884   1174
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1066
  helix:  1.12 (0.21), residues: 564
  sheet:  0.55 (0.44), residues: 138
  loop : -0.59 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 293 
 TYR   0.019   0.002   TYR A 373 
 PHE   0.035   0.002   PHE A  14 
 TRP   0.022   0.002   TRP A 110 
 HIS   0.004   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9232)
  covalent geometry    : angle       0.60546 (12422)
  hydrogen bonds       : bond        0.05597 (  481)
  hydrogen bonds       : angle       5.11185 ( 1443)
  metal coordination   : bond        0.00387 (    4)

*********************** 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
  223 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 220
  time to evaluate  : 0.390 
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    5 LEU cc_start: 0.9139 (tp) cc_final: 0.8884 (tp)
REVERT: A   19 LEU cc_start: 0.9352 (mt) cc_final: 0.8835 (mt)
REVERT: A   27 LYS cc_start: 0.9286 (tttm) cc_final: 0.9072 (tppt)
REVERT: A  129 LYS cc_start: 0.9006 (pttt) cc_final: 0.8687 (pttm)
REVERT: A  143 LYS cc_start: 0.8822 (tttt) cc_final: 0.8492 (tptt)
REVERT: A  150 LEU cc_start: 0.8691 (tp) cc_final: 0.8432 (tp)
REVERT: A  180 ILE cc_start: 0.7856 (mt) cc_final: 0.7444 (mm)
REVERT: A  211 THR cc_start: 0.8774 (p) cc_final: 0.8289 (t)
REVERT: A  213 HIS cc_start: 0.8424 (m90) cc_final: 0.7848 (m90)
REVERT: A  227 ASN cc_start: 0.8090 (t0) cc_final: 0.7732 (t0)
REVERT: A  240 ASP cc_start: 0.8544 (m-30) cc_final: 0.8254 (m-30)
REVERT: A  260 THR cc_start: 0.8544 (p) cc_final: 0.8255 (p)
REVERT: A  263 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8542 (mt-10)
REVERT: A  265 ILE cc_start: 0.8578 (mm) cc_final: 0.8353 (mm)
REVERT: A  300 GLU cc_start: 0.9115 (tp30) cc_final: 0.8050 (tm-30)
REVERT: A  321 LEU cc_start: 0.9359 (mt) cc_final: 0.9142 (mt)
REVERT: A  330 MET cc_start: 0.6197 (ppp) cc_final: 0.5449 (tmm)
REVERT: A  494 MET cc_start: 0.8606 (ptm) cc_final: 0.8234 (ppp)
REVERT: B    5 LEU cc_start: 0.8730 (mp) cc_final: 0.8423 (mp)
REVERT: B    9 ILE cc_start: 0.8848 (mt) cc_final: 0.8010 (mt)
REVERT: B   12 PHE cc_start: 0.9285 (t80) cc_final: 0.8482 (t80)
REVERT: B   19 LEU cc_start: 0.9335 (mt) cc_final: 0.9010 (mt)
REVERT: B   31 ASN cc_start: 0.8701 (m-40) cc_final: 0.8333 (p0)
REVERT: B  137 TYR cc_start: 0.7493 (p90) cc_final: 0.6904 (p90)
REVERT: B  138 LEU cc_start: 0.6298 (tp) cc_final: 0.5882 (tp)
REVERT: B  143 LYS cc_start: 0.8688 (tttt) cc_final: 0.8172 (tttp)
REVERT: B  227 ASN cc_start: 0.7939 (t0) cc_final: 0.7630 (t0)
REVERT: B  240 ASP cc_start: 0.8488 (m-30) cc_final: 0.8191 (m-30)
REVERT: B  265 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8188 (mp)
REVERT: B  300 GLU cc_start: 0.9116 (tp30) cc_final: 0.8021 (tm-30)
REVERT: B  321 LEU cc_start: 0.9270 (mt) cc_final: 0.9050 (mt)
REVERT: B  330 MET cc_start: 0.6101 (tmm) cc_final: 0.5279 (tmm)
REVERT: B  339 TYR cc_start: 0.7401 (t80) cc_final: 0.7005 (t80)
REVERT: B  365 MET cc_start: 0.1242 (tpt) cc_final: 0.0986 (tpt)
REVERT: B  494 MET cc_start: 0.8525 (ttp) cc_final: 0.7997 (ptm)
REVERT: B  497 GLN cc_start: 0.8427 (mm110) cc_final: 0.7671 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 222
  average time/residue: 0.0966
  time to fit residues: 29.7833
Evaluate side-chains
  188 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 85 optimal weight:   30.0000
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
B 153 HIS
B 484 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.204999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.146191 restraints weight = 21905.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.147104 restraints weight = 14539.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.149365 restraints weight = 9951.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.150056 restraints weight = 8214.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.150754 restraints weight = 7046.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.5350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9236  Z= 0.144
  Angle     :  0.595   8.326  12422  Z= 0.326
  Chirality :  0.043   0.155   1358
  Planarity :  0.003   0.032   1520
  Dihedral  :  4.773  18.576   1174
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.58 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.26), residues: 1066
  helix:  1.11 (0.21), residues: 574
  sheet:  0.45 (0.46), residues: 136
  loop : -0.83 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 293 
 TYR   0.023   0.002   TYR B 553 
 PHE   0.036   0.002   PHE A  21 
 TRP   0.030   0.002   TRP A  99 
 HIS   0.004   0.001   HIS A 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9232)
  covalent geometry    : angle       0.59494 (12422)
  hydrogen bonds       : bond        0.05041 (  481)
  hydrogen bonds       : angle       5.08195 ( 1443)
  metal coordination   : bond        0.00534 (    4)

*********************** 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
  213 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.379 
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    1 MET cc_start: 0.5070 (ttt) cc_final: 0.4333 (tpp)
REVERT: A   19 LEU cc_start: 0.9432 (mt) cc_final: 0.8900 (mt)
REVERT: A  129 LYS cc_start: 0.9065 (pttt) cc_final: 0.8721 (pptt)
REVERT: A  137 TYR cc_start: 0.7340 (p90) cc_final: 0.6845 (p90)
REVERT: A  143 LYS cc_start: 0.9006 (tttt) cc_final: 0.8534 (tptt)
REVERT: A  150 LEU cc_start: 0.9040 (tp) cc_final: 0.8770 (tp)
REVERT: A  180 ILE cc_start: 0.7787 (mt) cc_final: 0.7442 (mm)
REVERT: A  213 HIS cc_start: 0.8350 (m90) cc_final: 0.7931 (m90)
REVERT: A  227 ASN cc_start: 0.8263 (t0) cc_final: 0.7926 (t0)
REVERT: A  247 ARG cc_start: 0.8516 (tmm-80) cc_final: 0.8315 (tmm-80)
REVERT: A  265 ILE cc_start: 0.8632 (mm) cc_final: 0.8378 (mm)
REVERT: A  293 ARG cc_start: 0.8318 (mtt90) cc_final: 0.8082 (mtm-85)
REVERT: A  300 GLU cc_start: 0.9214 (tp30) cc_final: 0.8135 (tm-30)
REVERT: A  321 LEU cc_start: 0.9421 (mt) cc_final: 0.9214 (mt)
REVERT: A  330 MET cc_start: 0.6667 (ppp) cc_final: 0.5688 (tmm)
REVERT: B    9 ILE cc_start: 0.8863 (mt) cc_final: 0.7778 (mt)
REVERT: B   19 LEU cc_start: 0.9464 (mt) cc_final: 0.9035 (mt)
REVERT: B   31 ASN cc_start: 0.8934 (m-40) cc_final: 0.8511 (p0)
REVERT: B  126 LEU cc_start: 0.9252 (mm) cc_final: 0.8585 (mm)
REVERT: B  137 TYR cc_start: 0.7648 (p90) cc_final: 0.7008 (p90)
REVERT: B  138 LEU cc_start: 0.6447 (tp) cc_final: 0.5904 (tp)
REVERT: B  143 LYS cc_start: 0.8679 (tttt) cc_final: 0.8143 (tttp)
REVERT: B  213 HIS cc_start: 0.8231 (m90) cc_final: 0.7722 (m90)
REVERT: B  263 GLU cc_start: 0.8174 (pm20) cc_final: 0.7905 (pm20)
REVERT: B  300 GLU cc_start: 0.9136 (tp30) cc_final: 0.8278 (tm-30)
REVERT: B  321 LEU cc_start: 0.9342 (mt) cc_final: 0.9133 (mt)
REVERT: B  330 MET cc_start: 0.6270 (tmm) cc_final: 0.5448 (tmm)
REVERT: B  339 TYR cc_start: 0.7556 (t80) cc_final: 0.7152 (t80)
REVERT: B  365 MET cc_start: 0.0770 (tpt) cc_final: -0.0942 (tpt)
REVERT: B  494 MET cc_start: 0.8500 (ttp) cc_final: 0.8132 (ptm)
REVERT: B  497 GLN cc_start: 0.8520 (mm110) cc_final: 0.7433 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1032
  time to fit residues: 30.0927
Evaluate side-chains
  184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 90 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 95 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
B 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.204185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.141958 restraints weight = 21513.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.146088 restraints weight = 14061.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.149965 restraints weight = 8579.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.151099 restraints weight = 6402.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.151241 restraints weight = 5241.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.5868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9236  Z= 0.155
  Angle     :  0.603   6.850  12422  Z= 0.327
  Chirality :  0.043   0.164   1358
  Planarity :  0.003   0.031   1520
  Dihedral  :  4.732  17.732   1174
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.26), residues: 1066
  helix:  1.21 (0.22), residues: 570
  sheet:  0.54 (0.46), residues: 136
  loop : -0.86 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 294 
 TYR   0.025   0.002   TYR B 394 
 PHE   0.027   0.002   PHE A 442 
 TRP   0.021   0.002   TRP A 110 
 HIS   0.004   0.001   HIS B 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9232)
  covalent geometry    : angle       0.60271 (12422)
  hydrogen bonds       : bond        0.04930 (  481)
  hydrogen bonds       : angle       5.00295 ( 1443)
  metal coordination   : bond        0.00622 (    4)

*********************** 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
  214 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.355 
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   19 LEU cc_start: 0.9479 (mt) cc_final: 0.8994 (mt)
REVERT: A  137 TYR cc_start: 0.7363 (p90) cc_final: 0.6950 (p90)
REVERT: A  143 LYS cc_start: 0.8935 (tttt) cc_final: 0.8466 (tptt)
REVERT: A  150 LEU cc_start: 0.9022 (tp) cc_final: 0.8777 (tp)
REVERT: A  210 ASP cc_start: 0.8731 (m-30) cc_final: 0.8412 (m-30)
REVERT: A  213 HIS cc_start: 0.8234 (m90) cc_final: 0.7802 (m90)
REVERT: A  217 PHE cc_start: 0.9217 (t80) cc_final: 0.8875 (t80)
REVERT: A  227 ASN cc_start: 0.8199 (t0) cc_final: 0.7894 (t0)
REVERT: A  250 LEU cc_start: 0.9611 (mt) cc_final: 0.9322 (mt)
REVERT: A  265 ILE cc_start: 0.8582 (mm) cc_final: 0.8345 (mm)
REVERT: A  300 GLU cc_start: 0.9254 (tp30) cc_final: 0.8415 (tm-30)
REVERT: A  321 LEU cc_start: 0.9373 (mt) cc_final: 0.9089 (mt)
REVERT: A  325 GLN cc_start: 0.9299 (pm20) cc_final: 0.8937 (pm20)
REVERT: A  330 MET cc_start: 0.6344 (ppp) cc_final: 0.5089 (tmm)
REVERT: A  368 MET cc_start: 0.4516 (mpp) cc_final: 0.4289 (mpp)
REVERT: B    1 MET cc_start: 0.5602 (ttt) cc_final: 0.5336 (ttt)
REVERT: B   15 ILE cc_start: 0.9231 (mm) cc_final: 0.8887 (mm)
REVERT: B   19 LEU cc_start: 0.9443 (mt) cc_final: 0.9021 (tp)
REVERT: B   31 ASN cc_start: 0.8832 (m-40) cc_final: 0.8537 (p0)
REVERT: B  126 LEU cc_start: 0.9188 (mm) cc_final: 0.8599 (mm)
REVERT: B  137 TYR cc_start: 0.7615 (p90) cc_final: 0.7339 (p90)
REVERT: B  138 LEU cc_start: 0.6858 (tp) cc_final: 0.6629 (tp)
REVERT: B  143 LYS cc_start: 0.8687 (tttt) cc_final: 0.8162 (tttp)
REVERT: B  210 ASP cc_start: 0.8711 (m-30) cc_final: 0.8465 (m-30)
REVERT: B  213 HIS cc_start: 0.8267 (m90) cc_final: 0.7750 (m90)
REVERT: B  217 PHE cc_start: 0.9241 (t80) cc_final: 0.8871 (t80)
REVERT: B  227 ASN cc_start: 0.8137 (t0) cc_final: 0.7675 (t0)
REVERT: B  263 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7858 (pm20)
REVERT: B  300 GLU cc_start: 0.9270 (tp30) cc_final: 0.8412 (tm-30)
REVERT: B  321 LEU cc_start: 0.9349 (mt) cc_final: 0.9120 (mt)
REVERT: B  330 MET cc_start: 0.6053 (tmm) cc_final: 0.5344 (tmm)
REVERT: B  339 TYR cc_start: 0.7496 (t80) cc_final: 0.7068 (t80)
REVERT: B  365 MET cc_start: 0.0909 (tpt) cc_final: -0.0833 (tpt)
REVERT: B  494 MET cc_start: 0.8354 (ttp) cc_final: 0.8084 (ttt)
REVERT: B  497 GLN cc_start: 0.8784 (mm110) cc_final: 0.7906 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0975
  time to fit residues: 28.4425
Evaluate side-chains
  185 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 96 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0070
   chunk 99 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    3.0006

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 158 ASN
A 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.199198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.140884 restraints weight = 21755.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.142684 restraints weight = 13002.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.142886 restraints weight = 8931.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.143560 restraints weight = 8004.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.145546 restraints weight = 6970.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.6317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9236  Z= 0.203
  Angle     :  0.678   8.038  12422  Z= 0.371
  Chirality :  0.046   0.173   1358
  Planarity :  0.004   0.036   1520
  Dihedral  :  5.106  19.072   1174
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.26), residues: 1066
  helix:  0.80 (0.21), residues: 582
  sheet:  0.32 (0.49), residues: 120
  loop : -1.19 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 294 
 TYR   0.016   0.002   TYR B 441 
 PHE   0.015   0.002   PHE A 442 
 TRP   0.024   0.002   TRP A 110 
 HIS   0.005   0.002   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 9232)
  covalent geometry    : angle       0.67813 (12422)
  hydrogen bonds       : bond        0.05403 (  481)
  hydrogen bonds       : angle       5.36203 ( 1443)
  metal coordination   : bond        0.00917 (    4)

*********************** 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
  221 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.369 
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   15 ILE cc_start: 0.9359 (mm) cc_final: 0.9085 (mm)
REVERT: A  109 ILE cc_start: 0.8874 (pt) cc_final: 0.8665 (pt)
REVERT: A  126 LEU cc_start: 0.9233 (mm) cc_final: 0.8610 (mm)
REVERT: A  128 LEU cc_start: 0.9453 (mt) cc_final: 0.8892 (mm)
REVERT: A  143 LYS cc_start: 0.9066 (tttt) cc_final: 0.8557 (tptt)
REVERT: A  150 LEU cc_start: 0.9034 (tp) cc_final: 0.8800 (tp)
REVERT: A  210 ASP cc_start: 0.8554 (m-30) cc_final: 0.8230 (m-30)
REVERT: A  213 HIS cc_start: 0.7990 (m90) cc_final: 0.7755 (m90)
REVERT: A  227 ASN cc_start: 0.7565 (t0) cc_final: 0.7219 (t0)
REVERT: A  250 LEU cc_start: 0.9603 (mt) cc_final: 0.9337 (mt)
REVERT: A  265 ILE cc_start: 0.8769 (mm) cc_final: 0.8448 (mm)
REVERT: A  293 ARG cc_start: 0.8411 (mtt90) cc_final: 0.8205 (mtm-85)
REVERT: A  321 LEU cc_start: 0.9453 (mt) cc_final: 0.9213 (mt)
REVERT: A  336 ASP cc_start: 0.7791 (p0) cc_final: 0.7577 (p0)
REVERT: B   12 PHE cc_start: 0.9282 (t80) cc_final: 0.8935 (t80)
REVERT: B   15 ILE cc_start: 0.9513 (mm) cc_final: 0.8944 (mm)
REVERT: B  126 LEU cc_start: 0.9220 (mm) cc_final: 0.8631 (mm)
REVERT: B  137 TYR cc_start: 0.7862 (p90) cc_final: 0.7508 (p90)
REVERT: B  143 LYS cc_start: 0.8939 (tttt) cc_final: 0.8556 (tttp)
REVERT: B  210 ASP cc_start: 0.8552 (m-30) cc_final: 0.8271 (m-30)
REVERT: B  213 HIS cc_start: 0.7980 (m90) cc_final: 0.7772 (m90)
REVERT: B  217 PHE cc_start: 0.9158 (t80) cc_final: 0.8595 (t80)
REVERT: B  227 ASN cc_start: 0.7952 (t0) cc_final: 0.7478 (t0)
REVERT: B  321 LEU cc_start: 0.9449 (mt) cc_final: 0.9215 (mt)
REVERT: B  325 GLN cc_start: 0.9117 (pm20) cc_final: 0.8799 (pm20)
REVERT: B  330 MET cc_start: 0.6370 (tmm) cc_final: 0.5638 (tmm)
REVERT: B  339 TYR cc_start: 0.7542 (t80) cc_final: 0.7314 (t80)
REVERT: B  365 MET cc_start: 0.0417 (tpt) cc_final: 0.0102 (tpt)
REVERT: B  494 MET cc_start: 0.8351 (ttp) cc_final: 0.7878 (ptm)
REVERT: B  497 GLN cc_start: 0.8948 (mm110) cc_final: 0.8116 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0984
  time to fit residues: 29.8378
Evaluate side-chains
  184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 88 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0040
   chunk 35 optimal weight:    6.9990
   chunk 87 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   overall best weight:    3.2000

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.198516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.135398 restraints weight = 21577.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.138518 restraints weight = 14772.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.142093 restraints weight = 9166.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.143601 restraints weight = 6690.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.143817 restraints weight = 5814.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.6786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9236  Z= 0.213
  Angle     :  0.715   7.197  12422  Z= 0.390
  Chirality :  0.047   0.177   1358
  Planarity :  0.005   0.045   1520
  Dihedral  :  5.271  20.178   1174
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.26), residues: 1066
  helix:  0.68 (0.21), residues: 584
  sheet:  0.50 (0.52), residues: 110
  loop : -1.50 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 247 
 TYR   0.017   0.002   TYR B 373 
 PHE   0.022   0.002   PHE A  21 
 TRP   0.042   0.003   TRP A  99 
 HIS   0.005   0.002   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 9232)
  covalent geometry    : angle       0.71547 (12422)
  hydrogen bonds       : bond        0.05515 (  481)
  hydrogen bonds       : angle       5.63177 ( 1443)
  metal coordination   : bond        0.00930 (    4)

*********************** 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
  198 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.369 
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: 0.9033 (t80) cc_final: 0.8682 (t80)
REVERT: A   15 ILE cc_start: 0.9223 (mm) cc_final: 0.8659 (mm)
REVERT: A  126 LEU cc_start: 0.9226 (mm) cc_final: 0.8673 (mm)
REVERT: A  143 LYS cc_start: 0.9040 (tttt) cc_final: 0.8632 (tptt)
REVERT: A  173 PHE cc_start: 0.7745 (t80) cc_final: 0.6951 (t80)
REVERT: A  210 ASP cc_start: 0.8593 (m-30) cc_final: 0.8220 (m-30)
REVERT: A  213 HIS cc_start: 0.8195 (m90) cc_final: 0.7820 (m90)
REVERT: A  227 ASN cc_start: 0.7546 (t0) cc_final: 0.6994 (t0)
REVERT: A  250 LEU cc_start: 0.9576 (mt) cc_final: 0.9289 (mt)
REVERT: A  265 ILE cc_start: 0.8700 (mm) cc_final: 0.8432 (mm)
REVERT: A  293 ARG cc_start: 0.8420 (mtt90) cc_final: 0.8199 (mtm-85)
REVERT: A  321 LEU cc_start: 0.9445 (mt) cc_final: 0.9209 (mt)
REVERT: A  330 MET cc_start: 0.4962 (ppp) cc_final: 0.4229 (ppp)
REVERT: A  365 MET cc_start: 0.0890 (tpt) cc_final: 0.0049 (tpt)
REVERT: A  368 MET cc_start: 0.4593 (mpp) cc_final: 0.4372 (mpp)
REVERT: A  493 ASN cc_start: 0.8798 (m-40) cc_final: 0.8571 (m-40)
REVERT: B    1 MET cc_start: 0.6588 (ttt) cc_final: 0.5897 (tpp)
REVERT: B   12 PHE cc_start: 0.9150 (t80) cc_final: 0.8879 (t80)
REVERT: B   15 ILE cc_start: 0.9548 (mm) cc_final: 0.9298 (mm)
REVERT: B  129 LYS cc_start: 0.8904 (pttt) cc_final: 0.8537 (pttm)
REVERT: B  137 TYR cc_start: 0.7929 (p90) cc_final: 0.7573 (p90)
REVERT: B  143 LYS cc_start: 0.8963 (tttt) cc_final: 0.8616 (tttp)
REVERT: B  173 PHE cc_start: 0.8097 (t80) cc_final: 0.7882 (t80)
REVERT: B  213 HIS cc_start: 0.8059 (m90) cc_final: 0.7808 (m90)
REVERT: B  227 ASN cc_start: 0.7376 (t0) cc_final: 0.6627 (t0)
REVERT: B  321 LEU cc_start: 0.9434 (mt) cc_final: 0.9177 (mt)
REVERT: B  330 MET cc_start: 0.5135 (tmm) cc_final: 0.4210 (tmm)
REVERT: B  365 MET cc_start: 0.0359 (tpt) cc_final: -0.0000 (tpt)
REVERT: B  494 MET cc_start: 0.8393 (ttp) cc_final: 0.7979 (ptm)
REVERT: B  497 GLN cc_start: 0.8649 (mm110) cc_final: 0.7619 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1048
  time to fit residues: 28.4674
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  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 96 optimal weight:   30.0000
   chunk 60 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 52 optimal weight:    7.9990
   chunk 43 optimal weight:   20.0000
   chunk 36 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.9184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.204711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.139448 restraints weight = 21585.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.144550 restraints weight = 12616.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.147903 restraints weight = 8551.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.150058 restraints weight = 6394.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.151455 restraints weight = 5207.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.7040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9236  Z= 0.127
  Angle     :  0.621  11.694  12422  Z= 0.331
  Chirality :  0.044   0.183   1358
  Planarity :  0.004   0.039   1520
  Dihedral  :  4.830  19.820   1174
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.26), residues: 1066
  helix:  1.09 (0.22), residues: 582
  sheet:  0.44 (0.51), residues: 114
  loop : -1.36 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 247 
 TYR   0.020   0.001   TYR B 337 
 PHE   0.018   0.001   PHE A 173 
 TRP   0.022   0.002   TRP A 110 
 HIS   0.006   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9232)
  covalent geometry    : angle       0.62118 (12422)
  hydrogen bonds       : bond        0.04690 (  481)
  hydrogen bonds       : angle       5.09200 ( 1443)
  metal coordination   : bond        0.00808 (    4)

*********************** 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
  199 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.9032 (t80) cc_final: 0.8474 (t80)
REVERT: A   15 ILE cc_start: 0.9278 (mm) cc_final: 0.8831 (mm)
REVERT: A  123 LYS cc_start: 0.7211 (ttpt) cc_final: 0.6597 (ptmm)
REVERT: A  129 LYS cc_start: 0.8806 (pttt) cc_final: 0.8528 (pttm)
REVERT: A  138 LEU cc_start: 0.7808 (tp) cc_final: 0.7408 (tt)
REVERT: A  143 LYS cc_start: 0.8993 (tttt) cc_final: 0.8639 (tptt)
REVERT: A  210 ASP cc_start: 0.8244 (m-30) cc_final: 0.7845 (m-30)
REVERT: A  217 PHE cc_start: 0.9158 (t80) cc_final: 0.8409 (t80)
REVERT: A  227 ASN cc_start: 0.7208 (t0) cc_final: 0.6709 (t0)
REVERT: A  265 ILE cc_start: 0.8620 (mm) cc_final: 0.8344 (mm)
REVERT: A  293 ARG cc_start: 0.8464 (mtt90) cc_final: 0.8210 (mtm-85)
REVERT: A  321 LEU cc_start: 0.9437 (mt) cc_final: 0.9180 (mt)
REVERT: A  330 MET cc_start: 0.3656 (ppp) cc_final: 0.2956 (ppp)
REVERT: A  493 ASN cc_start: 0.8854 (m-40) cc_final: 0.8644 (m-40)
REVERT: B   12 PHE cc_start: 0.9120 (t80) cc_final: 0.8806 (t80)
REVERT: B   15 ILE cc_start: 0.9433 (mm) cc_final: 0.9191 (mm)
REVERT: B  123 LYS cc_start: 0.7328 (ttpt) cc_final: 0.6740 (ptmm)
REVERT: B  126 LEU cc_start: 0.9056 (mm) cc_final: 0.8583 (mm)
REVERT: B  143 LYS cc_start: 0.8804 (tttt) cc_final: 0.8272 (tttp)
REVERT: B  217 PHE cc_start: 0.9150 (t80) cc_final: 0.8387 (t80)
REVERT: B  227 ASN cc_start: 0.8133 (t0) cc_final: 0.7093 (t0)
REVERT: B  300 GLU cc_start: 0.9352 (tp30) cc_final: 0.9023 (tm-30)
REVERT: B  321 LEU cc_start: 0.9442 (mt) cc_final: 0.9185 (mt)
REVERT: B  330 MET cc_start: 0.5135 (tmm) cc_final: 0.4172 (tmm)
REVERT: B  365 MET cc_start: -0.0195 (tpt) cc_final: -0.0464 (tpt)
REVERT: B  494 MET cc_start: 0.8630 (ttp) cc_final: 0.8344 (ptm)
REVERT: B  497 GLN cc_start: 0.8644 (mm110) cc_final: 0.7843 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0992
  time to fit residues: 27.1944
Evaluate side-chains
  169 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0270
   chunk 32 optimal weight:   20.0000
   chunk 33 optimal weight:    0.4980
   chunk 35 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:   30.0000
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.3042

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.204298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.139561 restraints weight = 21876.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.144581 restraints weight = 13019.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.147789 restraints weight = 8927.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.150000 restraints weight = 6738.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.151375 restraints weight = 5494.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.7274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9236  Z= 0.134
  Angle     :  0.627   9.597  12422  Z= 0.336
  Chirality :  0.044   0.182   1358
  Planarity :  0.003   0.037   1520
  Dihedral  :  4.713  18.270   1174
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.26), residues: 1066
  helix:  1.14 (0.22), residues: 582
  sheet:  0.38 (0.51), residues: 114
  loop : -1.40 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 247 
 TYR   0.017   0.001   TYR A 552 
 PHE   0.023   0.002   PHE A 173 
 TRP   0.026   0.002   TRP A 110 
 HIS   0.006   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9232)
  covalent geometry    : angle       0.62656 (12422)
  hydrogen bonds       : bond        0.04692 (  481)
  hydrogen bonds       : angle       5.13452 ( 1443)
  metal coordination   : bond        0.00558 (    4)

*********************** 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
  196 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.232 
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   15 ILE cc_start: 0.9302 (mm) cc_final: 0.8919 (mm)
REVERT: A  129 LYS cc_start: 0.8866 (pttt) cc_final: 0.8559 (pttm)
REVERT: A  143 LYS cc_start: 0.9018 (tttt) cc_final: 0.8639 (tptt)
REVERT: A  210 ASP cc_start: 0.8236 (m-30) cc_final: 0.7853 (m-30)
REVERT: A  213 HIS cc_start: 0.8295 (m90) cc_final: 0.8091 (m90)
REVERT: A  217 PHE cc_start: 0.9169 (t80) cc_final: 0.8433 (t80)
REVERT: A  227 ASN cc_start: 0.7238 (t0) cc_final: 0.6865 (t0)
REVERT: A  265 ILE cc_start: 0.8601 (mm) cc_final: 0.8350 (mm)
REVERT: A  293 ARG cc_start: 0.8270 (mtt90) cc_final: 0.8051 (mtm-85)
REVERT: A  321 LEU cc_start: 0.9444 (mt) cc_final: 0.9188 (mt)
REVERT: A  330 MET cc_start: 0.4258 (ppp) cc_final: 0.3820 (ppp)
REVERT: A  365 MET cc_start: 0.0184 (tpt) cc_final: -0.1433 (tpt)
REVERT: A  493 ASN cc_start: 0.8839 (m-40) cc_final: 0.8635 (m-40)
REVERT: B    5 LEU cc_start: 0.8479 (mp) cc_final: 0.8233 (mm)
REVERT: B   12 PHE cc_start: 0.9119 (t80) cc_final: 0.8841 (t80)
REVERT: B   15 ILE cc_start: 0.9536 (mm) cc_final: 0.9332 (mm)
REVERT: B  123 LYS cc_start: 0.7459 (ttpt) cc_final: 0.6988 (ptmm)
REVERT: B  126 LEU cc_start: 0.9186 (mm) cc_final: 0.8881 (mm)
REVERT: B  128 LEU cc_start: 0.9433 (mt) cc_final: 0.9176 (mm)
REVERT: B  129 LYS cc_start: 0.8844 (pttt) cc_final: 0.8523 (pttm)
REVERT: B  143 LYS cc_start: 0.8795 (tttt) cc_final: 0.8485 (tttp)
REVERT: B  213 HIS cc_start: 0.8154 (m90) cc_final: 0.7552 (m90)
REVERT: B  217 PHE cc_start: 0.9179 (t80) cc_final: 0.8432 (t80)
REVERT: B  227 ASN cc_start: 0.8140 (t0) cc_final: 0.7161 (t0)
REVERT: B  321 LEU cc_start: 0.9463 (mt) cc_final: 0.9215 (mt)
REVERT: B  494 MET cc_start: 0.8611 (ttp) cc_final: 0.8322 (ptm)
REVERT: B  497 GLN cc_start: 0.8667 (mm110) cc_final: 0.7851 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0894
  time to fit residues: 24.3315
Evaluate side-chains
  169 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 49 optimal weight:   40.0000
   chunk 33 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0570
   overall best weight:    2.2702

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.201280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.140015 restraints weight = 22244.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.142216 restraints weight = 15723.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.145194 restraints weight = 9612.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.145849 restraints weight = 7874.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.146450 restraints weight = 6579.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.7517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9236  Z= 0.167
  Angle     :  0.661   8.172  12422  Z= 0.356
  Chirality :  0.045   0.170   1358
  Planarity :  0.004   0.033   1520
  Dihedral  :  4.845  18.173   1174
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.26), residues: 1066
  helix:  1.05 (0.22), residues: 584
  sheet:  0.28 (0.51), residues: 114
  loop : -1.49 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 247 
 TYR   0.016   0.002   TYR B 441 
 PHE   0.025   0.002   PHE A 173 
 TRP   0.023   0.002   TRP A  99 
 HIS   0.006   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9232)
  covalent geometry    : angle       0.66096 (12422)
  hydrogen bonds       : bond        0.04952 (  481)
  hydrogen bonds       : angle       5.25827 ( 1443)
  metal coordination   : bond        0.00843 (    4)

********************** 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
  183 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.370 
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   15 ILE cc_start: 0.9320 (mm) cc_final: 0.8940 (mm)
REVERT: A  126 LEU cc_start: 0.9129 (mm) cc_final: 0.8849 (mm)
REVERT: A  129 LYS cc_start: 0.8950 (pttt) cc_final: 0.8606 (pttm)
REVERT: A  143 LYS cc_start: 0.9090 (tttt) cc_final: 0.8722 (tptt)
REVERT: A  213 HIS cc_start: 0.8033 (m90) cc_final: 0.7615 (m90)
REVERT: A  217 PHE cc_start: 0.9263 (t80) cc_final: 0.8496 (t80)
REVERT: A  227 ASN cc_start: 0.7508 (t0) cc_final: 0.6869 (t0)
REVERT: A  250 LEU cc_start: 0.9472 (mt) cc_final: 0.9177 (mt)
REVERT: A  265 ILE cc_start: 0.8625 (mm) cc_final: 0.8336 (mm)
REVERT: A  293 ARG cc_start: 0.8413 (mtt90) cc_final: 0.8188 (mtm-85)
REVERT: A  321 LEU cc_start: 0.9451 (mt) cc_final: 0.9207 (mt)
REVERT: A  330 MET cc_start: 0.4855 (ppp) cc_final: 0.4288 (ppp)
REVERT: A  365 MET cc_start: 0.2675 (tpt) cc_final: 0.1094 (tpt)
REVERT: A  493 ASN cc_start: 0.8820 (m-40) cc_final: 0.8618 (m-40)
REVERT: B    5 LEU cc_start: 0.8801 (mp) cc_final: 0.8554 (mm)
REVERT: B   12 PHE cc_start: 0.9129 (t80) cc_final: 0.8853 (t80)
REVERT: B   15 ILE cc_start: 0.9547 (mm) cc_final: 0.9269 (mm)
REVERT: B  123 LYS cc_start: 0.7601 (ttpt) cc_final: 0.7024 (ptmm)
REVERT: B  126 LEU cc_start: 0.9277 (mm) cc_final: 0.8988 (mm)
REVERT: B  129 LYS cc_start: 0.8857 (pttt) cc_final: 0.8467 (pttm)
REVERT: B  143 LYS cc_start: 0.8878 (tttt) cc_final: 0.8514 (tttp)
REVERT: B  173 PHE cc_start: 0.7808 (t80) cc_final: 0.7332 (t80)
REVERT: B  217 PHE cc_start: 0.9248 (t80) cc_final: 0.8518 (t80)
REVERT: B  227 ASN cc_start: 0.8147 (t0) cc_final: 0.7223 (t0)
REVERT: B  321 LEU cc_start: 0.9447 (mt) cc_final: 0.9213 (mt)
REVERT: B  330 MET cc_start: 0.5235 (tmm) cc_final: 0.4385 (tmm)
REVERT: B  365 MET cc_start: 0.2952 (tpt) cc_final: 0.2316 (tpt)
REVERT: B  494 MET cc_start: 0.8611 (ttp) cc_final: 0.8326 (ptm)
REVERT: B  497 GLN cc_start: 0.8696 (mm110) cc_final: 0.7862 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0919
  time to fit residues: 23.4883
Evaluate side-chains
  162 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 64.4326 > 50:
  distance: 1 - 20:  30.691
  distance: 5 - 31:   6.913
  distance: 9 - 39:  38.018
  distance: 16 - 20:  29.542
  distance: 17 - 48:  35.256
  distance: 20 - 21:  45.406
  distance: 21 - 22:  40.581
  distance: 21 - 24:  33.442
  distance: 22 - 23:  42.188
  distance: 22 - 31:  32.698
  distance: 23 - 53:  35.653
  distance: 24 - 25:  48.423
  distance: 25 - 26:  33.346
  distance: 25 - 27:  24.433
  distance: 26 - 28:   8.598
  distance: 27 - 29:  13.138
  distance: 28 - 30:   8.988
  distance: 29 - 30:  13.507
  distance: 31 - 32:  24.735
  distance: 32 - 33:  43.348
  distance: 32 - 35:  20.987
  distance: 33 - 34:  32.167
  distance: 33 - 39:  28.636
  distance: 34 - 61:  41.535
  distance: 35 - 36:  46.841
  distance: 36 - 37:  41.428
  distance: 36 - 38:  27.201
  distance: 39 - 40:  28.048
  distance: 40 - 41:  27.781
  distance: 40 - 43:  45.200
  distance: 41 - 42:  49.665
  distance: 41 - 48:  56.399
  distance: 42 - 69:  22.867
  distance: 43 - 44:  16.265
  distance: 44 - 45:  56.621
  distance: 45 - 46:  54.329
  distance: 46 - 47:  15.767
  distance: 48 - 49:  40.091
  distance: 49 - 50:  42.755
  distance: 49 - 52:  10.434
  distance: 50 - 51:  56.092
  distance: 50 - 53:  38.970
  distance: 51 - 81:  51.346
  distance: 53 - 54:  37.183
  distance: 54 - 55:  39.240
  distance: 54 - 57:   3.515
  distance: 55 - 56:  19.244
  distance: 55 - 61:  36.628
  distance: 56 - 89:  30.913
  distance: 57 - 58:  21.875
  distance: 58 - 59:   7.930
  distance: 58 - 60:  18.698
  distance: 61 - 62:  33.992
  distance: 62 - 63:  38.637
  distance: 62 - 65:  34.554
  distance: 63 - 64:  30.897
  distance: 63 - 69:  47.744
  distance: 64 - 98:  32.596
  distance: 65 - 66:  54.397
  distance: 66 - 67:  30.017
  distance: 66 - 68:  35.699
  distance: 69 - 70:  30.109
  distance: 70 - 71:  20.050
  distance: 70 - 73:  38.474
  distance: 71 - 72:  35.551
  distance: 71 - 81:  46.013
  distance: 72 - 110:  24.295
  distance: 73 - 74:  26.822
  distance: 74 - 75:   7.782
  distance: 74 - 76:  10.773
  distance: 75 - 77:   9.978
  distance: 76 - 78:   7.304
  distance: 77 - 79:  31.787
  distance: 78 - 79:  30.796
  distance: 79 - 80:  16.141
  distance: 81 - 82:   6.076
  distance: 82 - 83:  35.756
  distance: 82 - 85:  34.179
  distance: 83 - 84:  18.479
  distance: 83 - 89:  41.984
  distance: 84 - 118:  23.853
  distance: 85 - 86:   8.682
  distance: 86 - 87:  29.683
  distance: 86 - 88:  27.680
  distance: 89 - 90:  10.843
  distance: 90 - 91:  44.247
  distance: 90 - 93:  14.394
  distance: 91 - 92:  34.624
  distance: 91 - 98:  24.759
  distance: 93 - 94:  19.645
  distance: 94 - 95:  20.378
  distance: 95 - 96:  10.008
  distance: 96 - 97:  18.302
  distance: 98 - 99:  15.950
  distance: 99 - 100:  12.462
  distance: 99 - 102:   8.228
  distance: 100 - 101:  22.633
  distance: 100 - 110:  26.613
  distance: 102 - 103:   4.130
  distance: 103 - 104:   7.562
  distance: 103 - 105:  12.016
  distance: 104 - 106:   9.863
  distance: 105 - 107:  13.313
  distance: 106 - 108:  17.745
  distance: 107 - 108:  16.257
  distance: 108 - 109:   5.162