Starting phenix.real_space_refine
on Tue Apr 29 22:37:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exp_28658/04_2025/8exp_28658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exp_28658/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exp_28658/04_2025/8exp_28658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exp_28658/04_2025/8exp_28658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exp_28658/04_2025/8exp_28658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exp_28658/04_2025/8exp_28658.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      38      5.16       5
     C    5928      2.51       5
     N    1484      2.21       5
     O    1572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9024
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4511
          Classifications: {'peptide': 539}
          Link IDs: {'PTRANS': 10, 'TRANS': 528}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.30, per 1000 atoms: 0.92
  Number of scatterers: 9024
  At special positions: 0
  Unit cell: (73.9927, 106.477, 135.353, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      38     16.00
     O    1572      8.00
     N    1484      7.00
     C    5928      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "


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

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      56.6% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 31
    Processing helix  chain 'A' and resid 35 through 38
    Processing helix  chain 'A' and resid 39 through 46
    Processing helix  chain 'A' and resid 99 through 133
      removed outlier: 3.514A  pdb=" N   LYS A 133 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 151
    Processing helix  chain 'A' and resid 184 through 189
    Processing helix  chain 'A' and resid 194 through 208
      removed outlier: 3.611A  pdb=" N   ASN A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 224
      removed outlier: 4.058A  pdb=" N   ILE A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 252
      removed outlier: 3.890A  pdb=" N   ILE A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS A 239 " --> pdb=" O   ARG A 235 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 5.479A  pdb=" N   ASN A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 256'
    Processing helix  chain 'A' and resid 257 through 268
      removed outlier: 3.798A  pdb=" N   SER A 268 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 308 through 327
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 387 through 390
    Processing helix  chain 'A' and resid 391 through 402
    Processing helix  chain 'A' and resid 429 through 436
    Processing helix  chain 'A' and resid 438 through 448
      removed outlier: 3.660A  pdb=" N   PHE A 442 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 461
    Processing helix  chain 'A' and resid 484 through 497
    Processing helix  chain 'A' and resid 502 through 513
    Processing helix  chain 'A' and resid 564 through 579
    Processing helix  chain 'B' and resid 2 through 31
    Processing helix  chain 'B' and resid 35 through 38
    Processing helix  chain 'B' and resid 39 through 46
    Processing helix  chain 'B' and resid 99 through 133
      removed outlier: 3.515A  pdb=" N   LYS B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
    Processing helix  chain 'B' and resid 184 through 189
    Processing helix  chain 'B' and resid 194 through 208
      removed outlier: 3.611A  pdb=" N   ASN B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 4.058A  pdb=" N   ILE B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 252
      removed outlier: 3.890A  pdb=" N   ILE B 238 " --> pdb=" O   LYS B 234 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS B 239 " --> pdb=" O   ARG B 235 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN B 252 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 256
      removed outlier: 5.479A  pdb=" N   ASN B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 253 through 256'
    Processing helix  chain 'B' and resid 257 through 268
      removed outlier: 3.798A  pdb=" N   SER B 268 " --> pdb=" O   SER B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 308 through 327
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 352 through 357
    Processing helix  chain 'B' and resid 379 through 382
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 391 through 402
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 438 through 448
      removed outlier: 3.660A  pdb=" N   PHE B 442 " --> pdb=" O   VAL B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 461
    Processing helix  chain 'B' and resid 484 through 497
    Processing helix  chain 'B' and resid 502 through 513
    Processing helix  chain 'B' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.440A  pdb=" N   GLU B 522 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   VAL B 545 " --> pdb=" O   GLU B 522 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   TYR B 524 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY B 543 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LYS B 526 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE B 541 " --> pdb=" O   LYS B 526 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY B 528 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY B 539 " --> pdb=" O   GLY B 528 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLY B 530 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS B 372 " --> pdb=" O   SER B 367 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 94
      removed outlier: 6.967A  pdb=" N   TYR B 521 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LYS B 517 " --> pdb=" O   TYR B 521 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU B 523 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137
      removed outlier: 6.638A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.820A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 372 " --> pdb=" O   SER A 367 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   VAL A 545 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU A 522 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   TYR A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   LYS A 517 " --> pdb=" O   TYR A 521 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.820A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 372 " --> pdb=" O   SER A 367 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   VAL A 545 " --> pdb=" O   GLU A 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU A 522 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 9.576A  pdb=" N   PHE B  90 " --> pdb=" O   GLY A 525 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   THR A 527 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 8.958A  pdb=" N   THR B  92 " --> pdb=" O   THR A 527 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   THR A 529 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   ILE B  94 " --> pdb=" O   THR A 529 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE A 531 " --> pdb=" O   ILE B  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 385
    Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 137
      removed outlier: 6.638A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ARG B 162 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 384 through 385

    508 hydrogen bonds defined for protein.
    1443 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 2.88 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.940
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.980
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1066
  helix:  0.31 (0.19), residues: 564
  sheet:  0.61 (0.44), residues: 138
  loop : -0.63 (0.34), residues: 364

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

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

*********************** 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  : 0.915 
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: 0.2540
  time to fit residues: 99.4518
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  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    3.5988

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.199519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.140059 restraints weight = 21126.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.142858 restraints weight = 13722.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.143887 restraints weight = 9029.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9236  Z= 0.261
  Angle     :  0.776   8.398  12422  Z= 0.430
  Chirality :  0.050   0.191   1358
  Planarity :  0.005   0.045   1520
  Dihedral  :  5.523  22.255   1174
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.98 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.25), residues: 1066
  helix:  0.51 (0.21), residues: 564
  sheet:  0.75 (0.47), residues: 124
  loop : -1.06 (0.31), residues: 378

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07268 (  481)
  hydrogen bonds       : angle       5.99161 ( 1443)
  metal coordination   : bond        0.00921 (    4)
  covalent geometry    : bond        0.00554 ( 9232)
  covalent geometry    : angle       0.77562 (12422)

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

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.9324 (mt) cc_final: 0.9087 (tp)
REVERT: A   19 LEU cc_start: 0.9504 (mt) cc_final: 0.9064 (mt)
REVERT: A  143 LYS cc_start: 0.8855 (tttt) cc_final: 0.8408 (tttp)
REVERT: A  220 PHE cc_start: 0.8558 (m-80) cc_final: 0.8285 (m-10)
REVERT: A  224 MET cc_start: 0.8300 (mpp) cc_final: 0.8009 (mmm)
REVERT: A  226 TYR cc_start: 0.6493 (p90) cc_final: 0.5832 (p90)
REVERT: A  265 ILE cc_start: 0.8416 (mm) cc_final: 0.8163 (mm)
REVERT: A  300 GLU cc_start: 0.9368 (tp30) cc_final: 0.8484 (tm-30)
REVERT: A  321 LEU cc_start: 0.9295 (mt) cc_final: 0.9003 (mt)
REVERT: A  330 MET cc_start: 0.5657 (ppp) cc_final: 0.5229 (tmm)
REVERT: A  497 GLN cc_start: 0.8293 (mm110) cc_final: 0.7910 (tm-30)
REVERT: B    5 LEU cc_start: 0.8794 (mp) cc_final: 0.8348 (tp)
REVERT: B   12 PHE cc_start: 0.9441 (t80) cc_final: 0.8837 (t80)
REVERT: B   19 LEU cc_start: 0.9452 (mt) cc_final: 0.9050 (mt)
REVERT: B   33 MET cc_start: 0.8525 (mmp) cc_final: 0.8179 (mmp)
REVERT: B   96 LYS cc_start: 0.7918 (tptt) cc_final: 0.7503 (tmtt)
REVERT: B  137 TYR cc_start: 0.7995 (p90) cc_final: 0.7585 (p90)
REVERT: B  143 LYS cc_start: 0.8878 (tttt) cc_final: 0.8464 (tttp)
REVERT: B  220 PHE cc_start: 0.8522 (m-80) cc_final: 0.8254 (m-10)
REVERT: B  224 MET cc_start: 0.8293 (mpp) cc_final: 0.7963 (mmm)
REVERT: B  226 TYR cc_start: 0.6820 (p90) cc_final: 0.5968 (p90)
REVERT: B  227 ASN cc_start: 0.7734 (t0) cc_final: 0.7295 (t0)
REVERT: B  265 ILE cc_start: 0.8527 (mp) cc_final: 0.8222 (mp)
REVERT: B  300 GLU cc_start: 0.9301 (tp30) cc_final: 0.8280 (tm-30)
REVERT: B  321 LEU cc_start: 0.9317 (mt) cc_final: 0.9065 (mt)
REVERT: B  339 TYR cc_start: 0.7192 (t80) cc_final: 0.6796 (t80)
REVERT: B  497 GLN cc_start: 0.8232 (mm110) cc_final: 0.7963 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2411
  time to fit residues: 70.8606
Evaluate side-chains
  175 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 89 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
A 484 ASN
B 144 ASN
B 302 ASN
B 537 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.201502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.138034 restraints weight = 21439.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.142976 restraints weight = 12516.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.146242 restraints weight = 8565.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.5029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9236  Z= 0.173
  Angle     :  0.629   5.860  12422  Z= 0.352
  Chirality :  0.046   0.198   1358
  Planarity :  0.004   0.039   1520
  Dihedral  :  5.099  20.354   1174
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1066
  helix:  0.83 (0.21), residues: 568
  sheet:  0.49 (0.45), residues: 138
  loop : -0.92 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 110 
 HIS   0.005   0.001   HIS A 282 
 PHE   0.039   0.003   PHE A  14 
 TYR   0.014   0.002   TYR B  29 
 ARG   0.003   0.000   ARG B 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06028 (  481)
  hydrogen bonds       : angle       5.39417 ( 1443)
  metal coordination   : bond        0.00593 (    4)
  covalent geometry    : bond        0.00364 ( 9232)
  covalent geometry    : angle       0.62908 (12422)

*********************** 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
  215 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.9175 (mt) cc_final: 0.8912 (tp)
REVERT: A    9 ILE cc_start: 0.8789 (mt) cc_final: 0.7722 (mt)
REVERT: A   19 LEU cc_start: 0.9480 (mt) cc_final: 0.8983 (mt)
REVERT: A   31 ASN cc_start: 0.8987 (m-40) cc_final: 0.8589 (p0)
REVERT: A  126 LEU cc_start: 0.9267 (mt) cc_final: 0.8788 (mt)
REVERT: A  143 LYS cc_start: 0.8932 (tttt) cc_final: 0.8576 (tttp)
REVERT: A  150 LEU cc_start: 0.9004 (tp) cc_final: 0.8758 (tp)
REVERT: A  210 ASP cc_start: 0.8802 (m-30) cc_final: 0.8483 (m-30)
REVERT: A  213 HIS cc_start: 0.8238 (m90) cc_final: 0.7826 (m90)
REVERT: A  220 PHE cc_start: 0.8374 (m-80) cc_final: 0.8089 (m-10)
REVERT: A  224 MET cc_start: 0.8342 (mpp) cc_final: 0.7999 (mmm)
REVERT: A  226 TYR cc_start: 0.6491 (p90) cc_final: 0.5881 (p90)
REVERT: A  263 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8506 (mt-10)
REVERT: A  265 ILE cc_start: 0.8613 (mm) cc_final: 0.8403 (mm)
REVERT: A  300 GLU cc_start: 0.9428 (tp30) cc_final: 0.8416 (tm-30)
REVERT: A  321 LEU cc_start: 0.9396 (mt) cc_final: 0.9052 (mt)
REVERT: A  325 GLN cc_start: 0.8985 (mp10) cc_final: 0.8779 (mp10)
REVERT: A  330 MET cc_start: 0.6307 (ppp) cc_final: 0.5828 (tmm)
REVERT: A  494 MET cc_start: 0.8627 (ptm) cc_final: 0.8216 (ppp)
REVERT: A  497 GLN cc_start: 0.8504 (mm110) cc_final: 0.7890 (tm-30)
REVERT: B    1 MET cc_start: 0.6459 (ttt) cc_final: 0.6173 (ttt)
REVERT: B    9 ILE cc_start: 0.8851 (mt) cc_final: 0.7971 (mt)
REVERT: B   12 PHE cc_start: 0.9473 (t80) cc_final: 0.8981 (t80)
REVERT: B   19 LEU cc_start: 0.9426 (mt) cc_final: 0.9151 (mt)
REVERT: B   31 ASN cc_start: 0.8826 (m-40) cc_final: 0.8564 (p0)
REVERT: B   33 MET cc_start: 0.8747 (mmp) cc_final: 0.8318 (mmp)
REVERT: B   90 PHE cc_start: 0.7053 (t80) cc_final: 0.6817 (t80)
REVERT: B  126 LEU cc_start: 0.9406 (mt) cc_final: 0.8956 (mt)
REVERT: B  137 TYR cc_start: 0.7927 (p90) cc_final: 0.7594 (p90)
REVERT: B  143 LYS cc_start: 0.8808 (tttt) cc_final: 0.8369 (tttp)
REVERT: B  213 HIS cc_start: 0.8154 (m90) cc_final: 0.7683 (m90)
REVERT: B  220 PHE cc_start: 0.8437 (m-80) cc_final: 0.8143 (m-10)
REVERT: B  224 MET cc_start: 0.8448 (mpp) cc_final: 0.8039 (mmm)
REVERT: B  227 ASN cc_start: 0.8275 (t0) cc_final: 0.8008 (t0)
REVERT: B  265 ILE cc_start: 0.8585 (mp) cc_final: 0.8302 (mp)
REVERT: B  300 GLU cc_start: 0.9355 (tp30) cc_final: 0.8280 (tm-30)
REVERT: B  321 LEU cc_start: 0.9370 (mt) cc_final: 0.9141 (mt)
REVERT: B  330 MET cc_start: 0.6155 (tmm) cc_final: 0.5287 (tmm)
REVERT: B  339 TYR cc_start: 0.7569 (t80) cc_final: 0.7168 (t80)
REVERT: B  365 MET cc_start: 0.1645 (tpt) cc_final: -0.0520 (mmm)
REVERT: B  494 MET cc_start: 0.8495 (ttp) cc_final: 0.8088 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.2195
  time to fit residues: 64.2768
Evaluate side-chains
  177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0170
   chunk 32 optimal weight:   20.0000
   chunk 81 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 104 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.1822

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.204599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.140903 restraints weight = 21041.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.145877 restraints weight = 12367.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.149083 restraints weight = 8467.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.5553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9236  Z= 0.133
  Angle     :  0.583   9.854  12422  Z= 0.317
  Chirality :  0.043   0.158   1358
  Planarity :  0.003   0.036   1520
  Dihedral  :  4.890  19.926   1174
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.47 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1066
  helix:  1.03 (0.21), residues: 582
  sheet:  0.51 (0.46), residues: 136
  loop : -0.97 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  99 
 HIS   0.003   0.001   HIS B 282 
 PHE   0.033   0.002   PHE B  14 
 TYR   0.013   0.002   TYR A 337 
 ARG   0.004   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05114 (  481)
  hydrogen bonds       : angle       5.12297 ( 1443)
  metal coordination   : bond        0.00395 (    4)
  covalent geometry    : bond        0.00283 ( 9232)
  covalent geometry    : angle       0.58290 (12422)

*********************** 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
  217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5195 (ttt) cc_final: 0.4402 (tpp)
REVERT: A    5 LEU cc_start: 0.9213 (mt) cc_final: 0.8973 (tp)
REVERT: A    9 ILE cc_start: 0.8843 (mt) cc_final: 0.7714 (mt)
REVERT: A   19 LEU cc_start: 0.9461 (mt) cc_final: 0.9134 (mt)
REVERT: A   31 ASN cc_start: 0.8936 (m-40) cc_final: 0.8523 (p0)
REVERT: A  126 LEU cc_start: 0.9245 (mt) cc_final: 0.9026 (mt)
REVERT: A  137 TYR cc_start: 0.7097 (p90) cc_final: 0.6605 (p90)
REVERT: A  150 LEU cc_start: 0.9002 (tp) cc_final: 0.8785 (tp)
REVERT: A  210 ASP cc_start: 0.8757 (m-30) cc_final: 0.8475 (m-30)
REVERT: A  224 MET cc_start: 0.8358 (mpp) cc_final: 0.7870 (mmm)
REVERT: A  226 TYR cc_start: 0.6418 (p90) cc_final: 0.5821 (p90)
REVERT: A  233 VAL cc_start: 0.8471 (t) cc_final: 0.8151 (p)
REVERT: A  263 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8499 (mt-10)
REVERT: A  265 ILE cc_start: 0.8438 (mm) cc_final: 0.8206 (mm)
REVERT: A  300 GLU cc_start: 0.9376 (tp30) cc_final: 0.8471 (tm-30)
REVERT: A  321 LEU cc_start: 0.9360 (mt) cc_final: 0.9086 (mt)
REVERT: A  325 GLN cc_start: 0.9090 (mp10) cc_final: 0.8777 (mp10)
REVERT: A  330 MET cc_start: 0.5798 (ppp) cc_final: 0.5396 (tmm)
REVERT: A  497 GLN cc_start: 0.8363 (mm110) cc_final: 0.7685 (tm-30)
REVERT: B    9 ILE cc_start: 0.8768 (mt) cc_final: 0.7871 (mt)
REVERT: B   12 PHE cc_start: 0.9392 (t80) cc_final: 0.8869 (t80)
REVERT: B   19 LEU cc_start: 0.9409 (mt) cc_final: 0.9107 (mt)
REVERT: B   31 ASN cc_start: 0.8808 (m-40) cc_final: 0.8586 (p0)
REVERT: B  126 LEU cc_start: 0.9200 (mt) cc_final: 0.8964 (mt)
REVERT: B  137 TYR cc_start: 0.7610 (p90) cc_final: 0.7288 (p90)
REVERT: B  143 LYS cc_start: 0.8840 (tttt) cc_final: 0.8348 (tttp)
REVERT: B  224 MET cc_start: 0.8333 (mpp) cc_final: 0.7833 (mmm)
REVERT: B  227 ASN cc_start: 0.8261 (t0) cc_final: 0.7973 (t0)
REVERT: B  233 VAL cc_start: 0.8493 (t) cc_final: 0.8183 (p)
REVERT: B  265 ILE cc_start: 0.8291 (mp) cc_final: 0.8043 (mp)
REVERT: B  300 GLU cc_start: 0.9385 (tp30) cc_final: 0.8437 (tm-30)
REVERT: B  321 LEU cc_start: 0.9389 (mt) cc_final: 0.9085 (mt)
REVERT: B  339 TYR cc_start: 0.7570 (t80) cc_final: 0.7147 (t80)
REVERT: B  365 MET cc_start: 0.0329 (tpt) cc_final: -0.1632 (tpt)
REVERT: B  495 MET cc_start: 0.7400 (mtt) cc_final: 0.7165 (mtp)
REVERT: B  497 GLN cc_start: 0.8549 (mm110) cc_final: 0.7760 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 216
  average time/residue: 0.2150
  time to fit residues: 63.8773
Evaluate side-chains
  182 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 90 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0670
   chunk 39 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 85 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   overall best weight:    1.3322

-------------------------------------------------------------------------------
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 = 0.4673 r_free = 0.4673 target = 0.204600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.144414 restraints weight = 21419.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.147846 restraints weight = 14429.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.148737 restraints weight = 8735.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.5950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9236  Z= 0.128
  Angle     :  0.568   6.348  12422  Z= 0.310
  Chirality :  0.043   0.154   1358
  Planarity :  0.003   0.035   1520
  Dihedral  :  4.739  18.734   1174
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.27), residues: 1066
  helix:  1.31 (0.22), residues: 582
  sheet:  0.57 (0.46), residues: 138
  loop : -0.94 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 110 
 HIS   0.003   0.001   HIS A 282 
 PHE   0.030   0.002   PHE B  14 
 TYR   0.024   0.002   TYR B 394 
 ARG   0.005   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04756 (  481)
  hydrogen bonds       : angle       5.00690 ( 1443)
  metal coordination   : bond        0.00457 (    4)
  covalent geometry    : bond        0.00268 ( 9232)
  covalent geometry    : angle       0.56773 (12422)

*********************** 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
  211 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.9473 (mt) cc_final: 0.9190 (mt)
REVERT: A   31 ASN cc_start: 0.9107 (m-40) cc_final: 0.8686 (p0)
REVERT: A  137 TYR cc_start: 0.7267 (p90) cc_final: 0.6756 (p90)
REVERT: A  150 LEU cc_start: 0.8994 (tp) cc_final: 0.8779 (tp)
REVERT: A  213 HIS cc_start: 0.8021 (m90) cc_final: 0.7774 (m90)
REVERT: A  224 MET cc_start: 0.8184 (mpp) cc_final: 0.7780 (mmm)
REVERT: A  227 ASN cc_start: 0.8289 (t0) cc_final: 0.8050 (t0)
REVERT: A  233 VAL cc_start: 0.8490 (t) cc_final: 0.8152 (p)
REVERT: A  263 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8367 (mt-10)
REVERT: A  265 ILE cc_start: 0.8461 (mm) cc_final: 0.8247 (mm)
REVERT: A  300 GLU cc_start: 0.9386 (tp30) cc_final: 0.8498 (tm-30)
REVERT: A  321 LEU cc_start: 0.9398 (mt) cc_final: 0.9022 (mt)
REVERT: A  325 GLN cc_start: 0.9079 (mp10) cc_final: 0.8639 (mp10)
REVERT: A  330 MET cc_start: 0.5769 (ppp) cc_final: 0.5130 (ppp)
REVERT: A  497 GLN cc_start: 0.9064 (mm110) cc_final: 0.8303 (tm-30)
REVERT: B   12 PHE cc_start: 0.9342 (t80) cc_final: 0.8844 (t80)
REVERT: B   19 LEU cc_start: 0.9435 (mt) cc_final: 0.9123 (mt)
REVERT: B   31 ASN cc_start: 0.8944 (m-40) cc_final: 0.8633 (p0)
REVERT: B  137 TYR cc_start: 0.7531 (p90) cc_final: 0.7243 (p90)
REVERT: B  143 LYS cc_start: 0.8850 (tttt) cc_final: 0.8379 (tttp)
REVERT: B  213 HIS cc_start: 0.8232 (m90) cc_final: 0.7922 (m90)
REVERT: B  224 MET cc_start: 0.8163 (mpp) cc_final: 0.7726 (mmm)
REVERT: B  227 ASN cc_start: 0.8344 (t0) cc_final: 0.7902 (t0)
REVERT: B  233 VAL cc_start: 0.8500 (t) cc_final: 0.8160 (p)
REVERT: B  265 ILE cc_start: 0.8234 (mp) cc_final: 0.8004 (mp)
REVERT: B  300 GLU cc_start: 0.9403 (tp30) cc_final: 0.8479 (tm-30)
REVERT: B  321 LEU cc_start: 0.9439 (mt) cc_final: 0.9198 (mt)
REVERT: B  325 GLN cc_start: 0.9193 (pm20) cc_final: 0.8760 (pm20)
REVERT: B  330 MET cc_start: 0.6321 (tmm) cc_final: 0.5319 (tmm)
REVERT: B  339 TYR cc_start: 0.7609 (t80) cc_final: 0.7170 (t80)
REVERT: B  365 MET cc_start: 0.0701 (tpt) cc_final: -0.1054 (tpt)
REVERT: B  495 MET cc_start: 0.7541 (mtt) cc_final: 0.7301 (mtp)
REVERT: B  497 GLN cc_start: 0.8768 (mm110) cc_final: 0.7692 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.2274
  time to fit residues: 65.5990
Evaluate side-chains
  177 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 67 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 36 optimal weight:   30.0000
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.4689 r_free = 0.4689 target = 0.205756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.141755 restraints weight = 21603.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.146982 restraints weight = 12490.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.150232 restraints weight = 8443.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.6259

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= 0.121
  Angle     :  0.548   6.601  12422  Z= 0.296
  Chirality :  0.042   0.160   1358
  Planarity :  0.003   0.033   1520
  Dihedral  :  4.645  18.136   1174
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.27), residues: 1066
  helix:  1.38 (0.22), residues: 586
  sheet:  0.58 (0.47), residues: 136
  loop : -1.04 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 110 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.014   0.001   PHE B 121 
 TYR   0.017   0.001   TYR B 394 
 ARG   0.003   0.000   ARG B 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04404 (  481)
  hydrogen bonds       : angle       4.96917 ( 1443)
  metal coordination   : bond        0.00556 (    4)
  covalent geometry    : bond        0.00259 ( 9232)
  covalent geometry    : angle       0.54795 (12422)

*********************** 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
  207 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9391 (mm) cc_final: 0.9136 (mm)
REVERT: A   19 LEU cc_start: 0.9449 (mt) cc_final: 0.9200 (mt)
REVERT: A   31 ASN cc_start: 0.8910 (m-40) cc_final: 0.8476 (p0)
REVERT: A  123 LYS cc_start: 0.7118 (ttpt) cc_final: 0.6823 (ptmm)
REVERT: A  126 LEU cc_start: 0.9174 (mm) cc_final: 0.8762 (mm)
REVERT: A  137 TYR cc_start: 0.7049 (p90) cc_final: 0.6578 (p90)
REVERT: A  150 LEU cc_start: 0.8881 (tp) cc_final: 0.8657 (tp)
REVERT: A  173 PHE cc_start: 0.6973 (t80) cc_final: 0.6448 (t80)
REVERT: A  224 MET cc_start: 0.8026 (mpp) cc_final: 0.7629 (mmm)
REVERT: A  227 ASN cc_start: 0.7851 (t0) cc_final: 0.7524 (t0)
REVERT: A  233 VAL cc_start: 0.8415 (t) cc_final: 0.8088 (p)
REVERT: A  263 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8342 (mt-10)
REVERT: A  265 ILE cc_start: 0.8423 (mm) cc_final: 0.8175 (mm)
REVERT: A  300 GLU cc_start: 0.9417 (tp30) cc_final: 0.8424 (tm-30)
REVERT: A  321 LEU cc_start: 0.9371 (mt) cc_final: 0.9120 (mt)
REVERT: A  322 MET cc_start: 0.9072 (mtt) cc_final: 0.8840 (mtt)
REVERT: A  330 MET cc_start: 0.4442 (ppp) cc_final: 0.3862 (ppp)
REVERT: A  365 MET cc_start: 0.1085 (tpt) cc_final: -0.0331 (tpt)
REVERT: A  497 GLN cc_start: 0.9196 (mm110) cc_final: 0.8564 (tm-30)
REVERT: B    5 LEU cc_start: 0.8516 (mp) cc_final: 0.7975 (tp)
REVERT: B   12 PHE cc_start: 0.9300 (t80) cc_final: 0.8772 (t80)
REVERT: B   15 ILE cc_start: 0.9410 (mm) cc_final: 0.9091 (mm)
REVERT: B   31 ASN cc_start: 0.8792 (m-40) cc_final: 0.8520 (p0)
REVERT: B   90 PHE cc_start: 0.7200 (t80) cc_final: 0.6769 (t80)
REVERT: B  126 LEU cc_start: 0.9147 (mm) cc_final: 0.8722 (mm)
REVERT: B  137 TYR cc_start: 0.7426 (p90) cc_final: 0.7212 (p90)
REVERT: B  143 LYS cc_start: 0.8911 (tttt) cc_final: 0.8462 (tttp)
REVERT: B  173 PHE cc_start: 0.7127 (t80) cc_final: 0.6872 (t80)
REVERT: B  224 MET cc_start: 0.8006 (mpp) cc_final: 0.7641 (mmm)
REVERT: B  227 ASN cc_start: 0.8383 (t0) cc_final: 0.7830 (t0)
REVERT: B  233 VAL cc_start: 0.8458 (t) cc_final: 0.8102 (p)
REVERT: B  321 LEU cc_start: 0.9413 (mt) cc_final: 0.9170 (mt)
REVERT: B  330 MET cc_start: 0.6054 (tmm) cc_final: 0.5264 (tmm)
REVERT: B  339 TYR cc_start: 0.7562 (t80) cc_final: 0.7129 (t80)
REVERT: B  365 MET cc_start: 0.0468 (tpt) cc_final: -0.1184 (tpt)
REVERT: B  495 MET cc_start: 0.7644 (mtt) cc_final: 0.7318 (mtp)
REVERT: B  497 GLN cc_start: 0.8855 (mm110) cc_final: 0.7952 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2185
  time to fit residues: 62.5071
Evaluate side-chains
  185 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 66 optimal weight:    0.1980
   chunk 87 optimal weight:   20.0000
   chunk 84 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
A 537 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.207832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.145969 restraints weight = 22072.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.150579 restraints weight = 14822.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.154783 restraints weight = 8698.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.6580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9236  Z= 0.112
  Angle     :  0.566   9.242  12422  Z= 0.298
  Chirality :  0.042   0.155   1358
  Planarity :  0.003   0.032   1520
  Dihedral  :  4.467  18.326   1174
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 1066
  helix:  1.41 (0.22), residues: 586
  sheet:  0.58 (0.47), residues: 138
  loop : -1.04 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 110 
 HIS   0.006   0.001   HIS A 201 
 PHE   0.014   0.001   PHE B 121 
 TYR   0.020   0.001   TYR A 337 
 ARG   0.003   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04190 (  481)
  hydrogen bonds       : angle       4.79827 ( 1443)
  metal coordination   : bond        0.00321 (    4)
  covalent geometry    : bond        0.00229 ( 9232)
  covalent geometry    : angle       0.56635 (12422)

*********************** 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
  209 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9365 (mm) cc_final: 0.8857 (mm)
REVERT: A   31 ASN cc_start: 0.8760 (m-40) cc_final: 0.8271 (p0)
REVERT: A  123 LYS cc_start: 0.7111 (ttpt) cc_final: 0.6794 (ptmm)
REVERT: A  126 LEU cc_start: 0.9263 (mm) cc_final: 0.8911 (mm)
REVERT: A  137 TYR cc_start: 0.7430 (p90) cc_final: 0.7193 (p90)
REVERT: A  150 LEU cc_start: 0.8905 (tp) cc_final: 0.8687 (tp)
REVERT: A  213 HIS cc_start: 0.8392 (m90) cc_final: 0.8128 (m90)
REVERT: A  224 MET cc_start: 0.7876 (mpp) cc_final: 0.7503 (mmm)
REVERT: A  227 ASN cc_start: 0.7763 (t0) cc_final: 0.7464 (t0)
REVERT: A  233 VAL cc_start: 0.8596 (t) cc_final: 0.8156 (p)
REVERT: A  259 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8441 (mmmm)
REVERT: A  263 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8345 (mt-10)
REVERT: A  265 ILE cc_start: 0.8490 (mm) cc_final: 0.8242 (mm)
REVERT: A  300 GLU cc_start: 0.9384 (tp30) cc_final: 0.8756 (tp30)
REVERT: A  321 LEU cc_start: 0.9395 (mt) cc_final: 0.9165 (mt)
REVERT: A  330 MET cc_start: 0.3396 (ppp) cc_final: 0.2973 (ppp)
REVERT: A  365 MET cc_start: 0.1019 (tpt) cc_final: -0.0459 (tpt)
REVERT: A  497 GLN cc_start: 0.9180 (mm110) cc_final: 0.8544 (tm-30)
REVERT: B   12 PHE cc_start: 0.9263 (t80) cc_final: 0.8565 (t80)
REVERT: B   96 LYS cc_start: 0.6892 (tptt) cc_final: 0.6578 (tmtt)
REVERT: B  123 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6611 (ptmm)
REVERT: B  129 LYS cc_start: 0.8640 (pttt) cc_final: 0.8131 (pttp)
REVERT: B  143 LYS cc_start: 0.8874 (tttt) cc_final: 0.8411 (tttp)
REVERT: B  213 HIS cc_start: 0.8134 (m90) cc_final: 0.7826 (m90)
REVERT: B  224 MET cc_start: 0.7897 (mpp) cc_final: 0.7532 (mmm)
REVERT: B  227 ASN cc_start: 0.7612 (t0) cc_final: 0.7155 (t0)
REVERT: B  233 VAL cc_start: 0.8562 (t) cc_final: 0.8224 (p)
REVERT: B  300 GLU cc_start: 0.9421 (tp30) cc_final: 0.8778 (tp30)
REVERT: B  321 LEU cc_start: 0.9417 (mt) cc_final: 0.9184 (mt)
REVERT: B  330 MET cc_start: 0.6179 (tmm) cc_final: 0.5412 (tmm)
REVERT: B  339 TYR cc_start: 0.7435 (t80) cc_final: 0.6899 (t80)
REVERT: B  365 MET cc_start: 0.0369 (tpt) cc_final: -0.1110 (tpt)
REVERT: B  495 MET cc_start: 0.7688 (mtt) cc_final: 0.7428 (mtp)
REVERT: B  497 GLN cc_start: 0.8840 (mm110) cc_final: 0.7953 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.2208
  time to fit residues: 63.0259
Evaluate side-chains
  182 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0570
   chunk 101 optimal weight:   30.0000
   chunk 56 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 90 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.2104

-------------------------------------------------------------------------------
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
B 278 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.201990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.139455 restraints weight = 22253.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.143445 restraints weight = 14410.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.147024 restraints weight = 8965.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.6817

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= 0.169
  Angle     :  0.630   7.429  12422  Z= 0.338
  Chirality :  0.044   0.172   1358
  Planarity :  0.004   0.029   1520
  Dihedral  :  4.699  18.155   1174
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.27), residues: 1066
  helix:  1.26 (0.22), residues: 586
  sheet:  0.32 (0.50), residues: 124
  loop : -1.28 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A  99 
 HIS   0.006   0.001   HIS A 205 
 PHE   0.028   0.002   PHE A 173 
 TYR   0.019   0.002   TYR B 175 
 ARG   0.005   0.001   ARG B 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04754 (  481)
  hydrogen bonds       : angle       5.13617 ( 1443)
  metal coordination   : bond        0.00849 (    4)
  covalent geometry    : bond        0.00360 ( 9232)
  covalent geometry    : angle       0.62994 (12422)

*********************** 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
  192 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.9457 (tp) cc_final: 0.9235 (tp)
REVERT: A  123 LYS cc_start: 0.7288 (ttpt) cc_final: 0.6809 (ptmm)
REVERT: A  126 LEU cc_start: 0.9334 (mm) cc_final: 0.8936 (mm)
REVERT: A  137 TYR cc_start: 0.7446 (p90) cc_final: 0.7223 (p90)
REVERT: A  138 LEU cc_start: 0.8481 (tp) cc_final: 0.8111 (tt)
REVERT: A  213 HIS cc_start: 0.8002 (m90) cc_final: 0.7743 (m90)
REVERT: A  227 ASN cc_start: 0.7826 (t0) cc_final: 0.7501 (t0)
REVERT: A  263 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8397 (mt-10)
REVERT: A  265 ILE cc_start: 0.8365 (mm) cc_final: 0.8122 (mm)
REVERT: A  321 LEU cc_start: 0.9461 (mt) cc_final: 0.9241 (mt)
REVERT: A  330 MET cc_start: 0.3953 (ppp) cc_final: 0.3555 (ppp)
REVERT: A  365 MET cc_start: 0.1074 (tpt) cc_final: -0.0320 (tpt)
REVERT: A  497 GLN cc_start: 0.9127 (mm110) cc_final: 0.8423 (tm-30)
REVERT: B   12 PHE cc_start: 0.9306 (t80) cc_final: 0.9005 (t80)
REVERT: B  123 LYS cc_start: 0.7284 (ttpt) cc_final: 0.6797 (ptmm)
REVERT: B  126 LEU cc_start: 0.9151 (mm) cc_final: 0.8609 (mm)
REVERT: B  143 LYS cc_start: 0.8895 (tttt) cc_final: 0.8463 (tttp)
REVERT: B  213 HIS cc_start: 0.8042 (m90) cc_final: 0.7829 (m90)
REVERT: B  227 ASN cc_start: 0.7702 (t0) cc_final: 0.7244 (t0)
REVERT: B  233 VAL cc_start: 0.8337 (t) cc_final: 0.7966 (p)
REVERT: B  321 LEU cc_start: 0.9487 (mt) cc_final: 0.9247 (mt)
REVERT: B  330 MET cc_start: 0.5860 (tmm) cc_final: 0.5192 (tmm)
REVERT: B  497 GLN cc_start: 0.8569 (mm110) cc_final: 0.7583 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2120
  time to fit residues: 56.1863
Evaluate side-chains
  165 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0000
   chunk 91 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 76 optimal weight:    0.4980
   chunk 49 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.8588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.206106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.143958 restraints weight = 21719.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.149119 restraints weight = 12742.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.152478 restraints weight = 8615.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.7047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9236  Z= 0.119
  Angle     :  0.609   9.542  12422  Z= 0.320
  Chirality :  0.043   0.169   1358
  Planarity :  0.003   0.030   1520
  Dihedral  :  4.537  17.941   1174
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.27), residues: 1066
  helix:  1.38 (0.22), residues: 586
  sheet:  0.33 (0.47), residues: 138
  loop : -1.14 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 174 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.040   0.002   PHE A 173 
 TYR   0.017   0.001   TYR B 394 
 ARG   0.005   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  481)
  hydrogen bonds       : angle       4.94325 ( 1443)
  metal coordination   : bond        0.00331 (    4)
  covalent geometry    : bond        0.00249 ( 9232)
  covalent geometry    : angle       0.60918 (12422)

*********************** 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
  199 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6032 (mmm) cc_final: 0.5294 (mmt)
REVERT: A   15 ILE cc_start: 0.9247 (mm) cc_final: 0.9019 (mm)
REVERT: A   19 LEU cc_start: 0.9602 (tp) cc_final: 0.9399 (tp)
REVERT: A   31 ASN cc_start: 0.8801 (m-40) cc_final: 0.8589 (p0)
REVERT: A  127 TYR cc_start: 0.8432 (t80) cc_final: 0.8132 (t80)
REVERT: A  129 LYS cc_start: 0.8838 (pttt) cc_final: 0.8603 (pttp)
REVERT: A  137 TYR cc_start: 0.7736 (p90) cc_final: 0.7507 (p90)
REVERT: A  227 ASN cc_start: 0.7463 (t0) cc_final: 0.7020 (t0)
REVERT: A  233 VAL cc_start: 0.8567 (t) cc_final: 0.8231 (p)
REVERT: A  259 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8492 (mmmm)
REVERT: A  263 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8370 (mt-10)
REVERT: A  265 ILE cc_start: 0.8377 (mm) cc_final: 0.8106 (mm)
REVERT: A  300 GLU cc_start: 0.9475 (tp30) cc_final: 0.8910 (tp30)
REVERT: A  325 GLN cc_start: 0.9383 (pm20) cc_final: 0.9129 (pm20)
REVERT: A  330 MET cc_start: 0.3569 (ppp) cc_final: 0.3041 (ppp)
REVERT: A  365 MET cc_start: 0.0120 (tpt) cc_final: -0.1468 (tpt)
REVERT: A  497 GLN cc_start: 0.9165 (mm110) cc_final: 0.8422 (tm-30)
REVERT: B    1 MET cc_start: 0.6112 (tpp) cc_final: 0.5700 (mmt)
REVERT: B   12 PHE cc_start: 0.9312 (t80) cc_final: 0.8699 (t80)
REVERT: B  123 LYS cc_start: 0.7326 (ttpt) cc_final: 0.6873 (ptmm)
REVERT: B  127 TYR cc_start: 0.8505 (t80) cc_final: 0.8087 (t80)
REVERT: B  129 LYS cc_start: 0.8804 (pttt) cc_final: 0.8281 (pttm)
REVERT: B  143 LYS cc_start: 0.8974 (tttt) cc_final: 0.8585 (tttp)
REVERT: B  227 ASN cc_start: 0.7706 (t0) cc_final: 0.7264 (t0)
REVERT: B  233 VAL cc_start: 0.8578 (t) cc_final: 0.8223 (p)
REVERT: B  321 LEU cc_start: 0.9450 (mt) cc_final: 0.9199 (mt)
REVERT: B  330 MET cc_start: 0.5787 (tmm) cc_final: 0.5164 (tmm)
REVERT: B  497 GLN cc_start: 0.8639 (mm110) cc_final: 0.7885 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2111
  time to fit residues: 57.8221
Evaluate side-chains
  174 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 26 optimal weight:    0.3980
   chunk 41 optimal weight:   20.0000
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 31 optimal weight:   20.0000
   overall best weight:    1.8384

-------------------------------------------------------------------------------
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 = 0.203908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.138870 restraints weight = 22307.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.143818 restraints weight = 13280.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.146956 restraints weight = 9136.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.7291

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= 0.150
  Angle     :  0.644   8.467  12422  Z= 0.341
  Chirality :  0.044   0.155   1358
  Planarity :  0.004   0.047   1520
  Dihedral  :  4.667  18.248   1174
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 1066
  helix:  1.30 (0.22), residues: 586
  sheet:  0.21 (0.50), residues: 124
  loop : -1.23 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A  99 
 HIS   0.004   0.001   HIS B 205 
 PHE   0.046   0.002   PHE A 173 
 TYR   0.020   0.002   TYR B 394 
 ARG   0.006   0.001   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04571 (  481)
  hydrogen bonds       : angle       5.14657 ( 1443)
  metal coordination   : bond        0.00557 (    4)
  covalent geometry    : bond        0.00328 ( 9232)
  covalent geometry    : angle       0.64378 (12422)

********************** 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
  193 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6012 (mmm) cc_final: 0.5183 (mmt)
REVERT: A   15 ILE cc_start: 0.9301 (mm) cc_final: 0.9031 (mm)
REVERT: A   31 ASN cc_start: 0.8841 (m-40) cc_final: 0.8618 (p0)
REVERT: A  126 LEU cc_start: 0.9136 (mm) cc_final: 0.8675 (mm)
REVERT: A  127 TYR cc_start: 0.8488 (t80) cc_final: 0.8200 (t80)
REVERT: A  213 HIS cc_start: 0.8027 (m90) cc_final: 0.7552 (m90)
REVERT: A  227 ASN cc_start: 0.7539 (t0) cc_final: 0.7135 (t0)
REVERT: A  233 VAL cc_start: 0.8273 (t) cc_final: 0.7945 (p)
REVERT: A  263 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8365 (mt-10)
REVERT: A  265 ILE cc_start: 0.8319 (mm) cc_final: 0.8079 (mm)
REVERT: A  321 LEU cc_start: 0.9448 (mt) cc_final: 0.9184 (mt)
REVERT: A  330 MET cc_start: 0.3723 (ppp) cc_final: 0.3449 (ppp)
REVERT: A  365 MET cc_start: 0.0661 (tpt) cc_final: -0.0989 (tpt)
REVERT: A  497 GLN cc_start: 0.9161 (mm110) cc_final: 0.8426 (tm-30)
REVERT: A  579 MET cc_start: 0.5781 (mmm) cc_final: 0.5240 (mpp)
REVERT: B    1 MET cc_start: 0.6296 (tpp) cc_final: 0.5676 (mmt)
REVERT: B    5 LEU cc_start: 0.8537 (mp) cc_final: 0.8232 (mm)
REVERT: B   12 PHE cc_start: 0.9264 (t80) cc_final: 0.8938 (t80)
REVERT: B  126 LEU cc_start: 0.9127 (mm) cc_final: 0.8833 (mm)
REVERT: B  127 TYR cc_start: 0.8552 (t80) cc_final: 0.8089 (t80)
REVERT: B  129 LYS cc_start: 0.8914 (pttt) cc_final: 0.8463 (pttp)
REVERT: B  143 LYS cc_start: 0.9002 (tttt) cc_final: 0.8625 (tttp)
REVERT: B  213 HIS cc_start: 0.8103 (m90) cc_final: 0.7634 (m90)
REVERT: B  217 PHE cc_start: 0.9183 (t80) cc_final: 0.8650 (t80)
REVERT: B  227 ASN cc_start: 0.7727 (t0) cc_final: 0.7269 (t0)
REVERT: B  233 VAL cc_start: 0.8324 (t) cc_final: 0.7989 (p)
REVERT: B  321 LEU cc_start: 0.9443 (mt) cc_final: 0.9207 (mt)
REVERT: B  330 MET cc_start: 0.5159 (tmm) cc_final: 0.4670 (tmm)
REVERT: B  365 MET cc_start: 0.1784 (tpt) cc_final: 0.1193 (tpt)
REVERT: B  497 GLN cc_start: 0.8638 (mm110) cc_final: 0.7764 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2108
  time to fit residues: 56.6298
Evaluate side-chains
  163 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.4697 r_free = 0.4697 target = 0.207492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.143117 restraints weight = 22259.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.148143 restraints weight = 13237.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.151293 restraints weight = 9095.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.7502

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= 0.118
  Angle     :  0.612   8.621  12422  Z= 0.320
  Chirality :  0.043   0.150   1358
  Planarity :  0.003   0.029   1520
  Dihedral  :  4.463  16.103   1174
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.27), residues: 1066
  helix:  1.36 (0.22), residues: 586
  sheet:  0.20 (0.50), residues: 122
  loop : -1.25 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A  99 
 HIS   0.004   0.001   HIS A 201 
 PHE   0.033   0.002   PHE A 173 
 TYR   0.015   0.001   TYR B 394 
 ARG   0.005   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04174 (  481)
  hydrogen bonds       : angle       4.94003 ( 1443)
  metal coordination   : bond        0.00367 (    4)
  covalent geometry    : bond        0.00251 ( 9232)
  covalent geometry    : angle       0.61223 (12422)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3534.60 seconds
wall clock time: 62 minutes 17.62 seconds (3737.62 seconds total)