Starting phenix.real_space_refine
on Thu Feb 13 12:18:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exp_28658/02_2025/8exp_28658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exp_28658/02_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_28658/02_2025/8exp_28658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exp_28658/02_2025/8exp_28658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exp_28658/02_2025/8exp_28658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exp_28658/02_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-5592/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: 7.89, per 1000 atoms: 0.87
  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: 2.33
  Conformation dependent library (CDL) restraints added in 984.2 milliseconds
  
  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: 1.10
  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: 2.83

  Time building geometry restraints manager: 2.69 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:             0.150
  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:          0.320
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     26.900
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4467
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.019   0.137   9232  Z= 1.212
  Angle     :  1.741  11.026  12422  Z= 1.196
  Chirality :  0.099   0.374   1358
  Planarity :  0.008   0.037   1520
  Dihedral  : 10.687  78.757   3454
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.38 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.39 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1066
  helix:  0.31 (0.19), residues: 564
  sheet:  0.61 (0.44), residues: 138
  loop : -0.63 (0.34), residues: 364

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

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

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 295
  time to evaluate  : 1.033 
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: 0.2654
  time to fit residues: 103.8143
Evaluate side-chains
  184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
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 = 0.140077 restraints weight = 21126.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.142824 restraints weight = 13725.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.143776 restraints weight = 9033.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.4131

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

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

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

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

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

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.9325 (mt) cc_final: 0.9087 (tp)
REVERT: A   19 LEU cc_start: 0.9502 (mt) cc_final: 0.9060 (mt)
REVERT: A  143 LYS cc_start: 0.8856 (tttt) cc_final: 0.8409 (tttp)
REVERT: A  220 PHE cc_start: 0.8565 (m-80) cc_final: 0.8290 (m-10)
REVERT: A  224 MET cc_start: 0.8301 (mpp) cc_final: 0.8009 (mmm)
REVERT: A  226 TYR cc_start: 0.6495 (p90) cc_final: 0.5828 (p90)
REVERT: A  265 ILE cc_start: 0.8407 (mm) cc_final: 0.8151 (mm)
REVERT: A  300 GLU cc_start: 0.9369 (tp30) cc_final: 0.8487 (tm-30)
REVERT: A  321 LEU cc_start: 0.9296 (mt) cc_final: 0.9006 (mt)
REVERT: A  330 MET cc_start: 0.5681 (ppp) cc_final: 0.5241 (tmm)
REVERT: A  497 GLN cc_start: 0.8293 (mm110) cc_final: 0.7911 (tm-30)
REVERT: B    5 LEU cc_start: 0.8794 (mp) cc_final: 0.8346 (tp)
REVERT: B   12 PHE cc_start: 0.9443 (t80) cc_final: 0.8839 (t80)
REVERT: B   19 LEU cc_start: 0.9450 (mt) cc_final: 0.9046 (mt)
REVERT: B   33 MET cc_start: 0.8537 (mmp) cc_final: 0.8190 (mmp)
REVERT: B   96 LYS cc_start: 0.7921 (tptt) cc_final: 0.7505 (tmtt)
REVERT: B  137 TYR cc_start: 0.8012 (p90) cc_final: 0.7600 (p90)
REVERT: B  143 LYS cc_start: 0.8879 (tttt) cc_final: 0.8466 (tttp)
REVERT: B  220 PHE cc_start: 0.8529 (m-80) cc_final: 0.8259 (m-10)
REVERT: B  224 MET cc_start: 0.8294 (mpp) cc_final: 0.7964 (mmm)
REVERT: B  226 TYR cc_start: 0.6814 (p90) cc_final: 0.5960 (p90)
REVERT: B  227 ASN cc_start: 0.7737 (t0) cc_final: 0.7294 (t0)
REVERT: B  265 ILE cc_start: 0.8517 (mp) cc_final: 0.8212 (mp)
REVERT: B  300 GLU cc_start: 0.9302 (tp30) cc_final: 0.8284 (tm-30)
REVERT: B  321 LEU cc_start: 0.9317 (mt) cc_final: 0.9066 (mt)
REVERT: B  339 TYR cc_start: 0.7201 (t80) cc_final: 0.6802 (t80)
REVERT: B  497 GLN cc_start: 0.8235 (mm110) cc_final: 0.7965 (mm110)
  outliers start: 1
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2301
  time to fit residues: 67.6530
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  : 1.169 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.4643 r_free = 0.4643 target = 0.201545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.142202 restraints weight = 21427.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.145099 restraints weight = 14117.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.147192 restraints weight = 8690.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9232  Z= 0.238
  Angle     :  0.625   5.869  12422  Z= 0.350
  Chirality :  0.046   0.194   1358
  Planarity :  0.004   0.039   1520
  Dihedral  :  5.088  20.263   1174
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 13.07
  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:  0.22 (0.26), residues: 1066
  helix:  0.84 (0.21), residues: 572
  sheet:  0.49 (0.45), residues: 138
  loop : -1.03 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 110 
 HIS   0.005   0.001   HIS A 282 
 PHE   0.041   0.003   PHE A  14 
 TYR   0.014   0.002   TYR B  29 
 ARG   0.003   0.000   ARG B 293 

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

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LEU cc_start: 0.9167 (mt) cc_final: 0.8907 (tp)
REVERT: A    9 ILE cc_start: 0.8772 (mt) cc_final: 0.7717 (mt)
REVERT: A   19 LEU cc_start: 0.9470 (mt) cc_final: 0.8974 (mt)
REVERT: A   31 ASN cc_start: 0.9066 (m-40) cc_final: 0.8641 (p0)
REVERT: A  126 LEU cc_start: 0.9268 (mt) cc_final: 0.8800 (mt)
REVERT: A  143 LYS cc_start: 0.8944 (tttt) cc_final: 0.8597 (tttp)
REVERT: A  150 LEU cc_start: 0.9039 (tp) cc_final: 0.8802 (tp)
REVERT: A  210 ASP cc_start: 0.8848 (m-30) cc_final: 0.8562 (m-30)
REVERT: A  213 HIS cc_start: 0.8219 (m90) cc_final: 0.7786 (m90)
REVERT: A  220 PHE cc_start: 0.8283 (m-80) cc_final: 0.7432 (m-10)
REVERT: A  224 MET cc_start: 0.8378 (mpp) cc_final: 0.7471 (mpp)
REVERT: A  226 TYR cc_start: 0.6502 (p90) cc_final: 0.5879 (p90)
REVERT: A  263 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8347 (mt-10)
REVERT: A  265 ILE cc_start: 0.8686 (mm) cc_final: 0.8465 (mm)
REVERT: A  300 GLU cc_start: 0.9420 (tp30) cc_final: 0.8427 (tm-30)
REVERT: A  321 LEU cc_start: 0.9400 (mt) cc_final: 0.9059 (mt)
REVERT: A  325 GLN cc_start: 0.9000 (mp10) cc_final: 0.8777 (mp10)
REVERT: A  330 MET cc_start: 0.6487 (ppp) cc_final: 0.5890 (tmm)
REVERT: A  494 MET cc_start: 0.8649 (ptm) cc_final: 0.8242 (ppp)
REVERT: A  497 GLN cc_start: 0.8496 (mm110) cc_final: 0.7887 (tm-30)
REVERT: B    1 MET cc_start: 0.6347 (ttt) cc_final: 0.6070 (ttt)
REVERT: B    9 ILE cc_start: 0.8839 (mt) cc_final: 0.7980 (mt)
REVERT: B   12 PHE cc_start: 0.9408 (t80) cc_final: 0.8898 (t80)
REVERT: B   19 LEU cc_start: 0.9424 (mt) cc_final: 0.9155 (mt)
REVERT: B   31 ASN cc_start: 0.8934 (m-40) cc_final: 0.8649 (p0)
REVERT: B   33 MET cc_start: 0.8856 (mmp) cc_final: 0.8409 (mmp)
REVERT: B   90 PHE cc_start: 0.7087 (t80) cc_final: 0.6856 (t80)
REVERT: B  126 LEU cc_start: 0.9400 (mt) cc_final: 0.8946 (mt)
REVERT: B  137 TYR cc_start: 0.7914 (p90) cc_final: 0.7587 (p90)
REVERT: B  143 LYS cc_start: 0.8822 (tttt) cc_final: 0.8390 (tttp)
REVERT: B  213 HIS cc_start: 0.8147 (m90) cc_final: 0.7661 (m90)
REVERT: B  220 PHE cc_start: 0.8386 (m-80) cc_final: 0.8092 (m-10)
REVERT: B  224 MET cc_start: 0.8454 (mpp) cc_final: 0.8040 (mmm)
REVERT: B  227 ASN cc_start: 0.8226 (t0) cc_final: 0.7968 (t0)
REVERT: B  265 ILE cc_start: 0.8577 (mp) cc_final: 0.8287 (mp)
REVERT: B  300 GLU cc_start: 0.9354 (tp30) cc_final: 0.8294 (tm-30)
REVERT: B  321 LEU cc_start: 0.9378 (mt) cc_final: 0.9174 (mt)
REVERT: B  330 MET cc_start: 0.6217 (tmm) cc_final: 0.5371 (tmm)
REVERT: B  339 TYR cc_start: 0.7587 (t80) cc_final: 0.7182 (t80)
REVERT: B  365 MET cc_start: 0.1691 (tpt) cc_final: -0.0384 (mmm)
REVERT: B  494 MET cc_start: 0.8494 (ttp) cc_final: 0.8103 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.2279
  time to fit residues: 66.4142
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  : 1.116 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   chunk 81 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 104 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4678 r_free = 0.4678 target = 0.204926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.142914 restraints weight = 21041.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.147642 restraints weight = 14165.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.151796 restraints weight = 8274.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.5574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9232  Z= 0.181
  Angle     :  0.576   9.631  12422  Z= 0.314
  Chirality :  0.043   0.157   1358
  Planarity :  0.003   0.036   1520
  Dihedral  :  4.865  19.871   1174
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  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:  0.48 (0.26), residues: 1066
  helix:  1.05 (0.21), residues: 582
  sheet:  0.54 (0.47), residues: 136
  loop : -0.95 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  99 
 HIS   0.003   0.001   HIS B 282 
 PHE   0.032   0.002   PHE B  14 
 TYR   0.012   0.002   TYR A 337 
 ARG   0.004   0.000   ARG A 293 

*********************** 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
  218 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.977 
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: 0.5569 (ttt) cc_final: 0.5355 (tpt)
REVERT: A   19 LEU cc_start: 0.9462 (mt) cc_final: 0.9147 (mt)
REVERT: A   31 ASN cc_start: 0.8905 (m-40) cc_final: 0.8498 (p0)
REVERT: A  126 LEU cc_start: 0.9245 (mt) cc_final: 0.9025 (mt)
REVERT: A  137 TYR cc_start: 0.7046 (p90) cc_final: 0.6563 (p90)
REVERT: A  150 LEU cc_start: 0.9022 (tp) cc_final: 0.8815 (tp)
REVERT: A  210 ASP cc_start: 0.8814 (m-30) cc_final: 0.8559 (m-30)
REVERT: A  224 MET cc_start: 0.8326 (mpp) cc_final: 0.7880 (mmm)
REVERT: A  227 ASN cc_start: 0.8304 (t0) cc_final: 0.8068 (t0)
REVERT: A  233 VAL cc_start: 0.8449 (t) cc_final: 0.8124 (p)
REVERT: A  263 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8478 (mt-10)
REVERT: A  265 ILE cc_start: 0.8444 (mm) cc_final: 0.8220 (mm)
REVERT: A  300 GLU cc_start: 0.9372 (tp30) cc_final: 0.8466 (tm-30)
REVERT: A  321 LEU cc_start: 0.9360 (mt) cc_final: 0.9086 (mt)
REVERT: A  325 GLN cc_start: 0.9103 (mp10) cc_final: 0.8777 (mp10)
REVERT: A  330 MET cc_start: 0.5857 (ppp) cc_final: 0.5400 (tmm)
REVERT: A  497 GLN cc_start: 0.8509 (mm110) cc_final: 0.7904 (tm-30)
REVERT: B    9 ILE cc_start: 0.8762 (mt) cc_final: 0.7847 (mt)
REVERT: B   12 PHE cc_start: 0.9381 (t80) cc_final: 0.8847 (t80)
REVERT: B   19 LEU cc_start: 0.9403 (mt) cc_final: 0.9119 (mt)
REVERT: B   31 ASN cc_start: 0.8794 (m-40) cc_final: 0.8581 (p0)
REVERT: B  126 LEU cc_start: 0.9204 (mt) cc_final: 0.8965 (mt)
REVERT: B  137 TYR cc_start: 0.7492 (p90) cc_final: 0.7213 (p90)
REVERT: B  143 LYS cc_start: 0.8833 (tttt) cc_final: 0.8342 (tttp)
REVERT: B  224 MET cc_start: 0.8329 (mpp) cc_final: 0.7862 (mmm)
REVERT: B  227 ASN cc_start: 0.8242 (t0) cc_final: 0.8030 (t0)
REVERT: B  233 VAL cc_start: 0.8478 (t) cc_final: 0.8163 (p)
REVERT: B  265 ILE cc_start: 0.8319 (mp) cc_final: 0.8069 (mp)
REVERT: B  300 GLU cc_start: 0.9395 (tp30) cc_final: 0.8454 (tm-30)
REVERT: B  321 LEU cc_start: 0.9399 (mt) cc_final: 0.9097 (mt)
REVERT: B  339 TYR cc_start: 0.7487 (t80) cc_final: 0.7065 (t80)
REVERT: B  365 MET cc_start: 0.0452 (tpt) cc_final: -0.1322 (tpt)
REVERT: B  495 MET cc_start: 0.7364 (mtt) cc_final: 0.7158 (mtp)
REVERT: B  497 GLN cc_start: 0.8503 (mm110) cc_final: 0.7744 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 217
  average time/residue: 0.2351
  time to fit residues: 69.9145
Evaluate side-chains
  184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 90 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 57 optimal weight:    0.6980
   chunk 85 optimal weight:   20.0000
   chunk 48 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4693 r_free = 0.4693 target = 0.206575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.148150 restraints weight = 21617.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.150811 restraints weight = 13454.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.151184 restraints weight = 8937.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.6028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9232  Z= 0.153
  Angle     :  0.551   6.587  12422  Z= 0.300
  Chirality :  0.042   0.150   1358
  Planarity :  0.003   0.035   1520
  Dihedral  :  4.642  19.109   1174
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.82 (0.27), residues: 1066
  helix:  1.38 (0.22), residues: 584
  sheet:  0.64 (0.47), residues: 136
  loop : -0.89 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 110 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.029   0.001   PHE B  14 
 TYR   0.023   0.002   TYR B 394 
 ARG   0.005   0.000   ARG B 247 

*********************** 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
  221 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9369 (mm) cc_final: 0.8723 (mm)
REVERT: A   31 ASN cc_start: 0.9029 (m-40) cc_final: 0.8537 (p0)
REVERT: A  123 LYS cc_start: 0.7577 (ttpt) cc_final: 0.7256 (ptmm)
REVERT: A  137 TYR cc_start: 0.7269 (p90) cc_final: 0.7054 (p90)
REVERT: A  150 LEU cc_start: 0.9129 (tp) cc_final: 0.8920 (tp)
REVERT: A  210 ASP cc_start: 0.8723 (m-30) cc_final: 0.8460 (m-30)
REVERT: A  213 HIS cc_start: 0.8300 (m90) cc_final: 0.8056 (m90)
REVERT: A  224 MET cc_start: 0.8167 (mpp) cc_final: 0.7834 (mmm)
REVERT: A  227 ASN cc_start: 0.7892 (t0) cc_final: 0.7593 (t0)
REVERT: A  233 VAL cc_start: 0.8367 (t) cc_final: 0.8004 (p)
REVERT: A  263 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8358 (mt-10)
REVERT: A  265 ILE cc_start: 0.8410 (mm) cc_final: 0.8190 (mm)
REVERT: A  300 GLU cc_start: 0.9368 (tp30) cc_final: 0.8488 (tm-30)
REVERT: A  321 LEU cc_start: 0.9368 (mt) cc_final: 0.9057 (mt)
REVERT: A  325 GLN cc_start: 0.9040 (mp10) cc_final: 0.8772 (mp10)
REVERT: A  330 MET cc_start: 0.5027 (ppp) cc_final: 0.4402 (ppp)
REVERT: A  497 GLN cc_start: 0.9074 (mm110) cc_final: 0.8301 (tm-30)
REVERT: B   19 LEU cc_start: 0.9430 (mt) cc_final: 0.9124 (mt)
REVERT: B   31 ASN cc_start: 0.8936 (m-40) cc_final: 0.8694 (p0)
REVERT: B  137 TYR cc_start: 0.7457 (p90) cc_final: 0.7204 (p90)
REVERT: B  143 LYS cc_start: 0.8850 (tttt) cc_final: 0.8392 (tttp)
REVERT: B  213 HIS cc_start: 0.8369 (m90) cc_final: 0.8039 (m90)
REVERT: B  224 MET cc_start: 0.8103 (mpp) cc_final: 0.7721 (mmm)
REVERT: B  227 ASN cc_start: 0.8295 (t0) cc_final: 0.7963 (t0)
REVERT: B  233 VAL cc_start: 0.8564 (t) cc_final: 0.8236 (p)
REVERT: B  265 ILE cc_start: 0.8294 (mp) cc_final: 0.8056 (mp)
REVERT: B  300 GLU cc_start: 0.9387 (tp30) cc_final: 0.8530 (tm-30)
REVERT: B  321 LEU cc_start: 0.9426 (mt) cc_final: 0.9163 (mt)
REVERT: B  330 MET cc_start: 0.6046 (tmm) cc_final: 0.5135 (tmm)
REVERT: B  339 TYR cc_start: 0.7644 (t80) cc_final: 0.7181 (t80)
REVERT: B  365 MET cc_start: 0.0440 (tpt) cc_final: -0.1351 (tpt)
REVERT: B  497 GLN cc_start: 0.8804 (mm110) cc_final: 0.7717 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2264
  time to fit residues: 68.5490
Evaluate side-chains
  186 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 92 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 158 ASN
A 278 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.203354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.138739 restraints weight = 21651.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.143749 restraints weight = 12736.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.147017 restraints weight = 8718.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.6347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9232  Z= 0.212
  Angle     :  0.580   6.325  12422  Z= 0.316
  Chirality :  0.043   0.165   1358
  Planarity :  0.003   0.033   1520
  Dihedral  :  4.677  18.636   1174
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.70 (0.27), residues: 1066
  helix:  1.31 (0.22), residues: 586
  sheet:  0.66 (0.47), residues: 138
  loop : -1.06 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 110 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.033   0.002   PHE B  14 
 TYR   0.016   0.002   TYR B 441 
 ARG   0.004   0.000   ARG B 162 

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

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9356 (mm) cc_final: 0.9096 (mm)
REVERT: A   31 ASN cc_start: 0.8864 (m-40) cc_final: 0.8583 (p0)
REVERT: A  123 LYS cc_start: 0.7112 (ttpt) cc_final: 0.6807 (ptmm)
REVERT: A  126 LEU cc_start: 0.9234 (mm) cc_final: 0.8800 (mm)
REVERT: A  137 TYR cc_start: 0.7513 (p90) cc_final: 0.7219 (p90)
REVERT: A  227 ASN cc_start: 0.7875 (t0) cc_final: 0.7558 (t0)
REVERT: A  233 VAL cc_start: 0.8621 (t) cc_final: 0.8298 (p)
REVERT: A  247 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8454 (tmm-80)
REVERT: A  263 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8344 (mt-10)
REVERT: A  265 ILE cc_start: 0.8443 (mm) cc_final: 0.8210 (mm)
REVERT: A  300 GLU cc_start: 0.9427 (tp30) cc_final: 0.8421 (tm-30)
REVERT: A  321 LEU cc_start: 0.9418 (mt) cc_final: 0.9141 (mt)
REVERT: A  325 GLN cc_start: 0.9006 (mp10) cc_final: 0.8795 (mp10)
REVERT: A  330 MET cc_start: 0.4224 (ppp) cc_final: 0.3562 (ppp)
REVERT: A  365 MET cc_start: 0.1409 (tpt) cc_final: 0.0002 (tpt)
REVERT: A  497 GLN cc_start: 0.9210 (mm110) cc_final: 0.8570 (tm-30)
REVERT: B   12 PHE cc_start: 0.9358 (t80) cc_final: 0.8904 (t80)
REVERT: B   19 LEU cc_start: 0.9436 (mt) cc_final: 0.9110 (mt)
REVERT: B   31 ASN cc_start: 0.8915 (m-40) cc_final: 0.8654 (p0)
REVERT: B  126 LEU cc_start: 0.9172 (mm) cc_final: 0.8759 (mm)
REVERT: B  137 TYR cc_start: 0.7505 (p90) cc_final: 0.7210 (p90)
REVERT: B  143 LYS cc_start: 0.8913 (tttt) cc_final: 0.8462 (tttp)
REVERT: B  227 ASN cc_start: 0.8200 (t0) cc_final: 0.7706 (t0)
REVERT: B  233 VAL cc_start: 0.8503 (t) cc_final: 0.8164 (p)
REVERT: B  300 GLU cc_start: 0.9470 (tp30) cc_final: 0.8565 (tm-30)
REVERT: B  321 LEU cc_start: 0.9437 (mt) cc_final: 0.9202 (mt)
REVERT: B  330 MET cc_start: 0.6178 (tmm) cc_final: 0.5330 (tmm)
REVERT: B  339 TYR cc_start: 0.7594 (t80) cc_final: 0.7156 (t80)
REVERT: B  365 MET cc_start: 0.0624 (tpt) cc_final: -0.1086 (tpt)
REVERT: B  495 MET cc_start: 0.7641 (mtt) cc_final: 0.7395 (mtp)
REVERT: B  497 GLN cc_start: 0.8885 (mm110) cc_final: 0.7980 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2281
  time to fit residues: 64.7302
Evaluate side-chains
  176 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 12 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 87 optimal weight:   20.0000
   chunk 84 optimal weight:    0.0570
   chunk 83 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5900

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.208396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.145951 restraints weight = 22039.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.150748 restraints weight = 14248.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.154139 restraints weight = 8482.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.6655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9232  Z= 0.150
  Angle     :  0.549   7.031  12422  Z= 0.291
  Chirality :  0.042   0.145   1358
  Planarity :  0.003   0.029   1520
  Dihedral  :  4.515  18.261   1174
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  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:  0.77 (0.27), residues: 1066
  helix:  1.39 (0.22), residues: 586
  sheet:  0.64 (0.46), residues: 138
  loop : -1.05 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 110 
 HIS   0.005   0.001   HIS B 201 
 PHE   0.032   0.001   PHE B  14 
 TYR   0.023   0.001   TYR A 337 
 ARG   0.003   0.000   ARG A 294 

*********************** 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
  210 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9228 (mm) cc_final: 0.8948 (mm)
REVERT: A   31 ASN cc_start: 0.8806 (m-40) cc_final: 0.8273 (p0)
REVERT: A  123 LYS cc_start: 0.7270 (ttpt) cc_final: 0.6914 (ptmm)
REVERT: A  126 LEU cc_start: 0.9312 (mm) cc_final: 0.8942 (mm)
REVERT: A  173 PHE cc_start: 0.7010 (t80) cc_final: 0.6731 (t80)
REVERT: A  210 ASP cc_start: 0.8745 (m-30) cc_final: 0.8402 (m-30)
REVERT: A  212 LEU cc_start: 0.8783 (tp) cc_final: 0.8582 (tp)
REVERT: A  213 HIS cc_start: 0.8310 (m90) cc_final: 0.7972 (m90)
REVERT: A  227 ASN cc_start: 0.7817 (t0) cc_final: 0.7526 (t0)
REVERT: A  233 VAL cc_start: 0.8538 (t) cc_final: 0.8167 (p)
REVERT: A  247 ARG cc_start: 0.8619 (tmm-80) cc_final: 0.8401 (tmm-80)
REVERT: A  263 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8509 (mt-10)
REVERT: A  265 ILE cc_start: 0.8493 (mm) cc_final: 0.8270 (mm)
REVERT: A  300 GLU cc_start: 0.9376 (tp30) cc_final: 0.8741 (tp30)
REVERT: A  321 LEU cc_start: 0.9386 (mt) cc_final: 0.9175 (mt)
REVERT: A  330 MET cc_start: 0.3492 (ppp) cc_final: 0.3078 (ppp)
REVERT: A  365 MET cc_start: 0.0989 (tpt) cc_final: -0.0309 (tpt)
REVERT: A  497 GLN cc_start: 0.9193 (mm110) cc_final: 0.8551 (tm-30)
REVERT: B    5 LEU cc_start: 0.8474 (mp) cc_final: 0.7866 (tp)
REVERT: B   12 PHE cc_start: 0.9328 (t80) cc_final: 0.8846 (t80)
REVERT: B   19 LEU cc_start: 0.9409 (mt) cc_final: 0.9139 (mt)
REVERT: B   31 ASN cc_start: 0.8857 (m-40) cc_final: 0.8578 (p0)
REVERT: B  123 LYS cc_start: 0.7200 (ttpt) cc_final: 0.6633 (ptmm)
REVERT: B  126 LEU cc_start: 0.9337 (mm) cc_final: 0.8962 (mm)
REVERT: B  143 LYS cc_start: 0.8837 (tttt) cc_final: 0.8332 (tttp)
REVERT: B  173 PHE cc_start: 0.6949 (t80) cc_final: 0.6675 (t80)
REVERT: B  213 HIS cc_start: 0.8239 (m90) cc_final: 0.8008 (m90)
REVERT: B  227 ASN cc_start: 0.7654 (t0) cc_final: 0.7177 (t0)
REVERT: B  233 VAL cc_start: 0.8563 (t) cc_final: 0.8215 (p)
REVERT: B  300 GLU cc_start: 0.9410 (tp30) cc_final: 0.8421 (tm-30)
REVERT: B  321 LEU cc_start: 0.9437 (mt) cc_final: 0.9222 (mt)
REVERT: B  330 MET cc_start: 0.6182 (tmm) cc_final: 0.5523 (tmm)
REVERT: B  365 MET cc_start: 0.0370 (tpt) cc_final: -0.1018 (tpt)
REVERT: B  495 MET cc_start: 0.7540 (mtt) cc_final: 0.7316 (mtp)
REVERT: B  497 GLN cc_start: 0.8880 (mm110) cc_final: 0.8088 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2247
  time to fit residues: 64.9210
Evaluate side-chains
  184 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 98 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 101 optimal weight:   30.0000
   chunk 56 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 90 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.4652 r_free = 0.4652 target = 0.202726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.137142 restraints weight = 22124.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.142130 restraints weight = 13098.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.145440 restraints weight = 9020.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.6896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9232  Z= 0.232
  Angle     :  0.614   7.824  12422  Z= 0.330
  Chirality :  0.044   0.167   1358
  Planarity :  0.003   0.028   1520
  Dihedral  :  4.611  17.214   1174
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 14.06
  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:  0.54 (0.27), residues: 1066
  helix:  1.29 (0.22), residues: 586
  sheet:  0.39 (0.49), residues: 124
  loop : -1.20 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  99 
 HIS   0.006   0.001   HIS A 205 
 PHE   0.035   0.002   PHE B  14 
 TYR   0.016   0.002   TYR B 394 
 ARG   0.004   0.001   ARG A 162 

*********************** 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
  197 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4825 (tpt) cc_final: 0.4198 (tpt)
REVERT: A   15 ILE cc_start: 0.9326 (mm) cc_final: 0.8981 (mm)
REVERT: A   31 ASN cc_start: 0.8897 (m-40) cc_final: 0.8650 (p0)
REVERT: A  123 LYS cc_start: 0.7347 (ttpt) cc_final: 0.6905 (ptmm)
REVERT: A  129 LYS cc_start: 0.8908 (pttt) cc_final: 0.8619 (pttm)
REVERT: A  210 ASP cc_start: 0.8715 (m-30) cc_final: 0.8122 (m-30)
REVERT: A  227 ASN cc_start: 0.7821 (t0) cc_final: 0.7491 (t0)
REVERT: A  247 ARG cc_start: 0.8642 (tmm-80) cc_final: 0.8418 (tmm-80)
REVERT: A  259 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8557 (mmmm)
REVERT: A  263 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8399 (mt-10)
REVERT: A  265 ILE cc_start: 0.8356 (mm) cc_final: 0.8112 (mm)
REVERT: A  321 LEU cc_start: 0.9416 (mt) cc_final: 0.9174 (mt)
REVERT: A  330 MET cc_start: 0.3220 (ppp) cc_final: 0.2767 (ppp)
REVERT: A  365 MET cc_start: 0.0709 (tpt) cc_final: -0.0624 (tpt)
REVERT: A  497 GLN cc_start: 0.9160 (mm110) cc_final: 0.8641 (mp10)
REVERT: A  577 LYS cc_start: 0.8229 (ptpp) cc_final: 0.7556 (mmtm)
REVERT: B   12 PHE cc_start: 0.9296 (t80) cc_final: 0.8990 (t80)
REVERT: B   31 ASN cc_start: 0.8962 (m-40) cc_final: 0.8687 (p0)
REVERT: B  123 LYS cc_start: 0.7271 (ttpt) cc_final: 0.6806 (ptmm)
REVERT: B  129 LYS cc_start: 0.8870 (pttt) cc_final: 0.8596 (pttm)
REVERT: B  143 LYS cc_start: 0.8888 (tttt) cc_final: 0.8502 (tttp)
REVERT: B  213 HIS cc_start: 0.8504 (m90) cc_final: 0.8234 (m90)
REVERT: B  227 ASN cc_start: 0.7634 (t0) cc_final: 0.7113 (t0)
REVERT: B  233 VAL cc_start: 0.8295 (t) cc_final: 0.7925 (p)
REVERT: B  321 LEU cc_start: 0.9489 (mt) cc_final: 0.9242 (mt)
REVERT: B  330 MET cc_start: 0.5835 (tmm) cc_final: 0.5142 (tmm)
REVERT: B  365 MET cc_start: 0.0514 (tpt) cc_final: -0.1113 (tpt)
REVERT: B  495 MET cc_start: 0.7651 (mtt) cc_final: 0.7347 (mtp)
REVERT: B  497 GLN cc_start: 0.8861 (mm110) cc_final: 0.7972 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2229
  time to fit residues: 59.6942
Evaluate side-chains
  170 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0070
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0570
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.5116

-------------------------------------------------------------------------------
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 = 0.4709 r_free = 0.4709 target = 0.208427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.146151 restraints weight = 22105.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.151281 restraints weight = 13088.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.154577 restraints weight = 8878.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.7194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9232  Z= 0.161
  Angle     :  0.597   8.236  12422  Z= 0.314
  Chirality :  0.042   0.144   1358
  Planarity :  0.003   0.028   1520
  Dihedral  :  4.427  16.150   1174
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  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:  0.78 (0.27), residues: 1066
  helix:  1.43 (0.22), residues: 586
  sheet:  0.51 (0.47), residues: 138
  loop : -1.05 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  99 
 HIS   0.007   0.001   HIS B 549 
 PHE   0.016   0.001   PHE A 121 
 TYR   0.015   0.001   TYR B 441 
 ARG   0.004   0.000   ARG B 162 

*********************** 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
  206 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4587 (tpt) cc_final: 0.3927 (tpt)
REVERT: A   12 PHE cc_start: 0.9140 (t80) cc_final: 0.8589 (t80)
REVERT: A   31 ASN cc_start: 0.8798 (m-40) cc_final: 0.8507 (p0)
REVERT: A   36 TYR cc_start: 0.7991 (p90) cc_final: 0.7625 (p90)
REVERT: A  129 LYS cc_start: 0.8817 (pttt) cc_final: 0.8455 (pttp)
REVERT: A  213 HIS cc_start: 0.8066 (m90) cc_final: 0.7685 (m90)
REVERT: A  227 ASN cc_start: 0.7312 (t0) cc_final: 0.6691 (t0)
REVERT: A  233 VAL cc_start: 0.8592 (t) cc_final: 0.8155 (p)
REVERT: A  247 ARG cc_start: 0.8540 (tmm-80) cc_final: 0.8315 (tmm-80)
REVERT: A  259 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8453 (mmmm)
REVERT: A  263 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8542 (mt-10)
REVERT: A  265 ILE cc_start: 0.8473 (mm) cc_final: 0.8230 (mm)
REVERT: A  300 GLU cc_start: 0.9453 (tp30) cc_final: 0.8887 (tp30)
REVERT: A  321 LEU cc_start: 0.9431 (mt) cc_final: 0.9231 (mt)
REVERT: A  325 GLN cc_start: 0.9318 (pm20) cc_final: 0.8995 (pm20)
REVERT: A  330 MET cc_start: 0.3285 (ppp) cc_final: 0.2867 (ppp)
REVERT: A  365 MET cc_start: -0.0050 (tpt) cc_final: -0.1474 (tpt)
REVERT: A  497 GLN cc_start: 0.9156 (mm110) cc_final: 0.8423 (tm-30)
REVERT: B   12 PHE cc_start: 0.9254 (t80) cc_final: 0.8686 (t80)
REVERT: B   15 ILE cc_start: 0.9299 (mm) cc_final: 0.9085 (mm)
REVERT: B   31 ASN cc_start: 0.8897 (m-40) cc_final: 0.8613 (p0)
REVERT: B  110 TRP cc_start: 0.7754 (t-100) cc_final: 0.7544 (t-100)
REVERT: B  127 TYR cc_start: 0.8381 (t80) cc_final: 0.8162 (t80)
REVERT: B  129 LYS cc_start: 0.8826 (pttt) cc_final: 0.8403 (pttp)
REVERT: B  143 LYS cc_start: 0.8972 (tttt) cc_final: 0.8606 (tttp)
REVERT: B  227 ASN cc_start: 0.7521 (t0) cc_final: 0.7035 (t0)
REVERT: B  233 VAL cc_start: 0.8554 (t) cc_final: 0.8208 (p)
REVERT: B  321 LEU cc_start: 0.9469 (mt) cc_final: 0.9230 (mt)
REVERT: B  330 MET cc_start: 0.6139 (tmm) cc_final: 0.5562 (tmm)
REVERT: B  495 MET cc_start: 0.7688 (mtt) cc_final: 0.7348 (mtp)
REVERT: B  497 GLN cc_start: 0.8815 (mm110) cc_final: 0.8152 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2143
  time to fit residues: 60.7412
Evaluate side-chains
  173 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0870
   chunk 41 optimal weight:   20.0000
   chunk 8 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.8300

-------------------------------------------------------------------------------
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 = 0.4702 r_free = 0.4702 target = 0.207334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.145379 restraints weight = 22032.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.150492 restraints weight = 12954.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.153583 restraints weight = 8788.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.7389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9232  Z= 0.164
  Angle     :  0.586   8.841  12422  Z= 0.309
  Chirality :  0.042   0.149   1358
  Planarity :  0.003   0.028   1520
  Dihedral  :  4.404  15.384   1174
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  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:  0.69 (0.27), residues: 1066
  helix:  1.44 (0.22), residues: 586
  sheet:  0.33 (0.50), residues: 124
  loop : -1.15 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A  99 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.015   0.001   PHE A 173 
 TYR   0.016   0.001   TYR B 366 
 ARG   0.005   0.000   ARG B 247 

********************** 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
  206 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.4624 (tpt) cc_final: 0.3745 (tpt)
REVERT: A   12 PHE cc_start: 0.9114 (t80) cc_final: 0.8534 (t80)
REVERT: A   31 ASN cc_start: 0.8761 (m-40) cc_final: 0.8481 (p0)
REVERT: A  129 LYS cc_start: 0.8817 (pttt) cc_final: 0.8598 (pttm)
REVERT: A  227 ASN cc_start: 0.7334 (t0) cc_final: 0.6800 (t0)
REVERT: A  259 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8478 (mmmm)
REVERT: A  263 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8383 (mt-10)
REVERT: A  265 ILE cc_start: 0.8390 (mm) cc_final: 0.8156 (mm)
REVERT: A  325 GLN cc_start: 0.9321 (pm20) cc_final: 0.9006 (pm20)
REVERT: A  330 MET cc_start: 0.3144 (ppp) cc_final: 0.2764 (ppp)
REVERT: A  368 MET cc_start: 0.3774 (mpp) cc_final: 0.3370 (pmm)
REVERT: A  497 GLN cc_start: 0.9160 (mm110) cc_final: 0.8422 (tm-30)
REVERT: B    1 MET cc_start: 0.6114 (mmm) cc_final: 0.5793 (mmt)
REVERT: B   12 PHE cc_start: 0.9209 (t80) cc_final: 0.8649 (t80)
REVERT: B   15 ILE cc_start: 0.9353 (mm) cc_final: 0.9139 (mm)
REVERT: B   31 ASN cc_start: 0.8891 (m-40) cc_final: 0.8604 (p0)
REVERT: B  110 TRP cc_start: 0.7916 (t-100) cc_final: 0.7619 (t-100)
REVERT: B  127 TYR cc_start: 0.8491 (t80) cc_final: 0.8174 (t80)
REVERT: B  129 LYS cc_start: 0.8853 (pttt) cc_final: 0.8608 (pttm)
REVERT: B  143 LYS cc_start: 0.8977 (tttt) cc_final: 0.8556 (tttp)
REVERT: B  213 HIS cc_start: 0.8296 (m90) cc_final: 0.7990 (m90)
REVERT: B  227 ASN cc_start: 0.7485 (t0) cc_final: 0.6986 (t0)
REVERT: B  233 VAL cc_start: 0.8569 (t) cc_final: 0.8195 (p)
REVERT: B  321 LEU cc_start: 0.9435 (mt) cc_final: 0.9191 (mt)
REVERT: B  330 MET cc_start: 0.6147 (tmm) cc_final: 0.5609 (tmm)
REVERT: B  365 MET cc_start: 0.3824 (tpt) cc_final: 0.3331 (tpt)
REVERT: B  368 MET cc_start: 0.5754 (mpp) cc_final: 0.5532 (mmm)
REVERT: B  494 MET cc_start: 0.8851 (ptm) cc_final: 0.8598 (ptm)
REVERT: B  497 GLN cc_start: 0.8805 (mm110) cc_final: 0.7988 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2151
  time to fit residues: 61.2681
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  : 1.060 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 4 optimal weight:    0.0770
   chunk 54 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0070
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.209274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.149096 restraints weight = 22598.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.153580 restraints weight = 15129.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.156676 restraints weight = 9132.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.7577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9232  Z= 0.161
  Angle     :  0.589   8.761  12422  Z= 0.309
  Chirality :  0.042   0.147   1358
  Planarity :  0.003   0.028   1520
  Dihedral  :  4.317  15.039   1174
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  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:  0.71 (0.27), residues: 1066
  helix:  1.49 (0.22), residues: 586
  sheet:  0.32 (0.50), residues: 124
  loop : -1.17 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A  99 
 HIS   0.005   0.001   HIS A 201 
 PHE   0.014   0.001   PHE B 491 
 TYR   0.014   0.001   TYR B 441 
 ARG   0.004   0.000   ARG B 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3227.08 seconds
wall clock time: 58 minutes 54.09 seconds (3534.09 seconds total)