Starting phenix.real_space_refine
on Sat Aug 23 02:29:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exs_28661/08_2025/8exs_28661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exs_28661/08_2025/8exs_28661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exs_28661/08_2025/8exs_28661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exs_28661/08_2025/8exs_28661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exs_28661/08_2025/8exs_28661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exs_28661/08_2025/8exs_28661.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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    6118      2.51       5
     N    1538      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9320
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 556, 4659
          Classifications: {'peptide': 556}
          Link IDs: {'PTRANS': 11, 'TRANS': 544}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.72, per 1000 atoms: 0.29
  Number of scatterers: 9320
  At special positions: 0
  Unit cell: (90.015, 90.015, 122.844, 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    1624      8.00
     N    1538      7.00
     C    6118      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 321.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 201 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 205 "
      pdb="  ZN B 701 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 201 "
        pdb="ZN    ZN B 701 " - pdb=" NE2 HIS B 205 "


  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      58.4% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 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 47 through 51
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 4.522A  pdb=" N   ILE A 105 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 5.088A  pdb=" N   LYS A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASN A 152 " --> pdb=" O   THR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 193 through 208
    Processing helix  chain 'A' and resid 209 through 224
    Processing helix  chain 'A' and resid 228 through 252
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 6.117A  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 271
      removed outlier: 3.632A  pdb=" N   VAL A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 307 through 327
      removed outlier: 4.298A  pdb=" N   LEU A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 377 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 421 through 425
    Processing helix  chain 'A' and resid 429 through 436
    Processing helix  chain 'A' and resid 438 through 449
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.529A  pdb=" N   THR A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 497
    Processing helix  chain 'A' and resid 502 through 513
      removed outlier: 3.616A  pdb=" N   SER A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
    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 47 through 51
    Processing helix  chain 'B' and resid 99 through 134
      removed outlier: 4.522A  pdb=" N   ILE B 105 " --> pdb=" O   SER B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 152
      removed outlier: 5.088A  pdb=" N   LYS B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE B 146 " --> pdb=" O   GLU B 142 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASN B 152 " --> pdb=" O   THR B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 193 through 208
    Processing helix  chain 'B' and resid 209 through 224
    Processing helix  chain 'B' and resid 228 through 252
    Processing helix  chain 'B' and resid 253 through 256
      removed outlier: 6.117A  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 271
      removed outlier: 3.632A  pdb=" N   VAL B 269 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 307 through 327
      removed outlier: 4.296A  pdb=" N   LEU B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 352 through 357
    Processing helix  chain 'B' and resid 377 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 421 through 425
    Processing helix  chain 'B' and resid 429 through 436
    Processing helix  chain 'B' and resid 438 through 449
    Processing helix  chain 'B' and resid 450 through 461
      removed outlier: 3.531A  pdb=" N   THR B 454 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 497
    Processing helix  chain 'B' and resid 502 through 513
      removed outlier: 3.617A  pdb=" N   SER B 512 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 513 " --> pdb=" O   LEU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164
      removed outlier: 6.597A  pdb=" N   VAL A 160 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ARG A 162 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350
      removed outlier: 6.898A  pdb=" N   ASP A 346 " --> pdb=" O   TYR A 373 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ILE A 375 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   GLN A 348 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   GLY A 530 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   GLY A 539 " --> pdb=" O   GLY A 528 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLY A 528 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE A 541 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LYS A 526 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLY A 543 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   TYR A 524 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.547A  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: 6.739A  pdb=" N   TYR A 521 " --> pdb=" O   LYS A 517 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LYS A 517 " --> pdb=" O   TYR A 521 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU A 523 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164
      removed outlier: 6.596A  pdb=" N   VAL B 160 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ARG B 162 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350
      removed outlier: 6.897A  pdb=" N   ASP B 346 " --> pdb=" O   TYR B 373 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE B 375 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLN B 348 " --> pdb=" O   ILE B 375 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   GLY B 530 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   GLY B 539 " --> pdb=" O   GLY B 528 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLY B 528 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   PHE B 541 " --> pdb=" O   LYS B 526 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LYS B 526 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLY B 543 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   TYR B 524 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL B 545 " --> pdb=" O   GLU B 522 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   GLU B 522 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 521 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B 517 " --> pdb=" O   TYR B 521 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B 523 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)

    489 hydrogen bonds defined for protein.
    1401 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1464
        1.30 -     1.43: 2855
        1.43 -     1.57: 5100
        1.57 -     1.70: 57
        1.70 -     1.84: 70
  Bond restraints: 9546
  Sorted by residual:
  bond pdb=" CB  HIS A 201 "
       pdb=" CG  HIS A 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.388  0.109 1.40e-02 5.10e+03 6.08e+01
  bond pdb=" CB  HIS B 201 "
       pdb=" CG  HIS B 201 "
    ideal  model  delta    sigma   weight residual
    1.497  1.389  0.108 1.40e-02 5.10e+03 6.00e+01
  bond pdb=" CB  PHE B 501 "
       pdb=" CG  PHE B 501 "
    ideal  model  delta    sigma   weight residual
    1.502  1.380  0.122 2.30e-02 1.89e+03 2.84e+01
  bond pdb=" CB  PHE A 501 "
       pdb=" CG  PHE A 501 "
    ideal  model  delta    sigma   weight residual
    1.502  1.381  0.121 2.30e-02 1.89e+03 2.78e+01
  bond pdb=" CB  HIS A 549 "
       pdb=" CG  HIS A 549 "
    ideal  model  delta    sigma   weight residual
    1.497  1.562 -0.065 1.40e-02 5.10e+03 2.17e+01
  ... (remaining 9541 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11080
        2.38 -     4.77: 1540
        4.77 -     7.15: 194
        7.15 -     9.54: 36
        9.54 -    11.92: 6
  Bond angle restraints: 12856
  Sorted by residual:
  angle pdb=" C   SER A 386 "
        pdb=" N   PRO A 387 "
        pdb=" CA  PRO A 387 "
      ideal   model   delta    sigma   weight residual
     119.56  128.94   -9.38 1.02e+00 9.61e-01 8.46e+01
  angle pdb=" C   SER B 386 "
        pdb=" N   PRO B 387 "
        pdb=" CA  PRO B 387 "
      ideal   model   delta    sigma   weight residual
     119.56  128.84   -9.28 1.02e+00 9.61e-01 8.29e+01
  angle pdb=" N   ILE A 222 "
        pdb=" CA  ILE A 222 "
        pdb=" C   ILE A 222 "
      ideal   model   delta    sigma   weight residual
     111.45  103.71    7.74 9.30e-01 1.16e+00 6.93e+01
  angle pdb=" N   ILE B 222 "
        pdb=" CA  ILE B 222 "
        pdb=" C   ILE B 222 "
      ideal   model   delta    sigma   weight residual
     111.45  103.78    7.67 9.30e-01 1.16e+00 6.81e+01
  angle pdb=" N   TYR A 521 "
        pdb=" CA  TYR A 521 "
        pdb=" C   TYR A 521 "
      ideal   model   delta    sigma   weight residual
     108.60  120.52  -11.92 1.46e+00 4.69e-01 6.67e+01
  ... (remaining 12851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 5462
       16.28 -    32.57: 183
       32.57 -    48.85: 37
       48.85 -    65.13: 20
       65.13 -    81.41: 6
  Dihedral angle restraints: 5708
    sinusoidal: 2376
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" C   ASN A 406 "
           pdb=" N   ASN A 406 "
           pdb=" CA  ASN A 406 "
           pdb=" CB  ASN A 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.18    9.58     0      2.50e+00 1.60e-01 1.47e+01
  dihedral pdb=" C   ASN B 406 "
           pdb=" N   ASN B 406 "
           pdb=" CA  ASN B 406 "
           pdb=" CB  ASN B 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.11    9.51     0      2.50e+00 1.60e-01 1.45e+01
  dihedral pdb=" CA  GLU A 202 "
           pdb=" CB  GLU A 202 "
           pdb=" CG  GLU A 202 "
           pdb=" CD  GLU A 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    4.59   55.41     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 5705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 765
       0.076 -    0.153: 463
       0.153 -    0.229: 148
       0.229 -    0.305: 10
       0.305 -    0.381: 8
  Chirality restraints: 1394
  Sorted by residual:
  chirality pdb=" CA  PHE A 220 "
            pdb=" N   PHE A 220 "
            pdb=" C   PHE A 220 "
            pdb=" CB  PHE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.64e+00
  chirality pdb=" CA  PHE B 220 "
            pdb=" N   PHE B 220 "
            pdb=" C   PHE B 220 "
            pdb=" CB  PHE B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  ILE B 515 "
            pdb=" N   ILE B 515 "
            pdb=" C   ILE B 515 "
            pdb=" CB  ILE B 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.80   -0.37 2.00e-01 2.50e+01 3.37e+00
  ... (remaining 1391 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 419 "    0.062 2.00e-02 2.50e+03   3.23e-02 2.09e+01
        pdb=" CG  TYR A 419 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 419 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 419 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 419 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 419 "    0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 419 "   -0.061 2.00e-02 2.50e+03   3.20e-02 2.05e+01
        pdb=" CG  TYR B 419 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 419 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 419 "    0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 419 "    0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 419 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 419 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 419 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 540 "    0.056 2.00e-02 2.50e+03   2.68e-02 1.79e+01
        pdb=" CG  TRP B 540 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 540 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 540 "   -0.025 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 540 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 540 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 540 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 540 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 540 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 540 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.36: 13
        2.36 -     2.99: 5681
        2.99 -     3.63: 14462
        3.63 -     4.26: 24287
        4.26 -     4.90: 37307
  Nonbonded interactions: 81750
  Sorted by model distance:
  nonbonded pdb=" CB  ASP A 422 "
            pdb=" CB  ASP B 422 "
     model   vdw
     1.722 3.840
  nonbonded pdb=" O   ALA A  91 "
            pdb=" CZ  PHE B 421 "
     model   vdw
     1.923 3.340
  nonbonded pdb=" CZ  PHE A 421 "
            pdb=" O   ALA B  91 "
     model   vdw
     1.924 3.340
  nonbonded pdb=" OE2 GLU B 242 "
            pdb="ZN    ZN B 701 "
     model   vdw
     2.099 2.230
  nonbonded pdb=" OE2 GLU A 242 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.099 2.230
  ... (remaining 81745 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: 0.02
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.520
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5053
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      :  0.020   0.227   9551  Z= 1.150
  Angle     :  1.722  11.922  12856  Z= 1.186
  Chirality :  0.099   0.381   1394
  Planarity :  0.009   0.041   1576
  Dihedral  : 10.181  81.415   3560
  Min Nonbonded Distance : 1.722

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.77 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.23), residues: 1104
  helix:  0.31 (0.19), residues: 594
  sheet:  0.08 (0.47), residues: 124
  loop : -0.07 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 384 
 TYR   0.062   0.010   TYR A 419 
 PHE   0.047   0.006   PHE A 274 
 TRP   0.056   0.008   TRP B 540 
 HIS   0.010   0.002   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.01995 ( 9546)
  covalent geometry    : angle       1.72157 (12856)
  hydrogen bonds       : bond        0.16118 (  489)
  hydrogen bonds       : angle       7.39130 ( 1401)
  metal coordination   : bond        0.02375 (    4)
  Misc. bond           : bond        0.22736 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 341
  time to evaluate  : 0.346 
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  173 PHE cc_start: 0.4322 (m-80) cc_final: 0.3598 (m-80)
REVERT: A  316 ILE cc_start: 0.7263 (tp) cc_final: 0.6910 (tp)
REVERT: A  320 LEU cc_start: 0.8007 (mt) cc_final: 0.7510 (tp)
REVERT: A  412 MET cc_start: 0.2881 (tpp) cc_final: 0.1904 (tpp)
REVERT: A  434 MET cc_start: 0.4727 (tpp) cc_final: 0.4362 (tpp)
REVERT: B  173 PHE cc_start: 0.4309 (m-80) cc_final: 0.3592 (m-80)
REVERT: B  316 ILE cc_start: 0.7205 (tp) cc_final: 0.6845 (tp)
REVERT: B  320 LEU cc_start: 0.8018 (mt) cc_final: 0.7504 (tp)
REVERT: B  412 MET cc_start: 0.3080 (tpp) cc_final: 0.2131 (tpp)
REVERT: B  434 MET cc_start: 0.4728 (tpp) cc_final: 0.4340 (tpp)
  outliers start: 6
  outliers final: 2
  residues processed: 343
  average time/residue: 0.0817
  time to fit residues: 38.8246
Evaluate side-chains
  202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
A 252 ASN
A 297 ASN
A 538 ASN
B 152 ASN
B 252 ASN
B 297 ASN
B 538 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.157986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.109959 restraints weight = 22845.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.113666 restraints weight = 14314.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.116332 restraints weight = 10261.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.118144 restraints weight = 8018.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.119417 restraints weight = 6718.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9551  Z= 0.236
  Angle     :  0.703   6.377  12856  Z= 0.402
  Chirality :  0.046   0.162   1394
  Planarity :  0.004   0.031   1576
  Dihedral  :  4.913  19.195   1212
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  2.60 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.24), residues: 1104
  helix:  0.87 (0.20), residues: 590
  sheet:  0.12 (0.48), residues: 128
  loop : -0.42 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 235 
 TYR   0.022   0.002   TYR A 203 
 PHE   0.031   0.003   PHE B  22 
 TRP   0.014   0.002   TRP B 424 
 HIS   0.007   0.002   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 9546)
  covalent geometry    : angle       0.70265 (12856)
  hydrogen bonds       : bond        0.06495 (  489)
  hydrogen bonds       : angle       5.74190 ( 1401)
  metal coordination   : bond        0.00549 (    4)
  Misc. bond           : bond        0.00313 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 283
  time to evaluate  : 0.315 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8735 (t80) cc_final: 0.8417 (t80)
REVERT: A  142 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8773 (mt-10)
REVERT: A  173 PHE cc_start: 0.6308 (m-80) cc_final: 0.5310 (m-80)
REVERT: A  188 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7491 (tmtt)
REVERT: A  195 LEU cc_start: 0.7977 (mm) cc_final: 0.7738 (mm)
REVERT: A  213 HIS cc_start: 0.8712 (m-70) cc_final: 0.8375 (m90)
REVERT: A  265 ILE cc_start: 0.7912 (mt) cc_final: 0.7694 (mt)
REVERT: A  297 ASN cc_start: 0.8372 (m110) cc_final: 0.8152 (m-40)
REVERT: A  310 ILE cc_start: 0.8867 (mt) cc_final: 0.8217 (tt)
REVERT: A  406 ASN cc_start: 0.7685 (p0) cc_final: 0.7451 (p0)
REVERT: A  434 MET cc_start: 0.7002 (tpp) cc_final: 0.6051 (tpp)
REVERT: A  476 MET cc_start: 0.5407 (ptm) cc_final: 0.4886 (ptt)
REVERT: B   12 PHE cc_start: 0.8731 (t80) cc_final: 0.8421 (t80)
REVERT: B  152 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8150 (m-40)
REVERT: B  173 PHE cc_start: 0.6329 (m-80) cc_final: 0.5314 (m-80)
REVERT: B  195 LEU cc_start: 0.7952 (mm) cc_final: 0.7681 (mm)
REVERT: B  213 HIS cc_start: 0.8696 (m-70) cc_final: 0.8371 (m90)
REVERT: B  265 ILE cc_start: 0.7906 (mt) cc_final: 0.7692 (mt)
REVERT: B  297 ASN cc_start: 0.8374 (m110) cc_final: 0.8125 (m-40)
REVERT: B  310 ILE cc_start: 0.8858 (mt) cc_final: 0.8069 (tt)
REVERT: B  406 ASN cc_start: 0.7710 (p0) cc_final: 0.7477 (p0)
REVERT: B  434 MET cc_start: 0.6996 (tpp) cc_final: 0.6041 (tpp)
REVERT: B  476 MET cc_start: 0.5224 (ptm) cc_final: 0.4727 (ptt)
  outliers start: 6
  outliers final: 2
  residues processed: 289
  average time/residue: 0.0735
  time to fit residues: 30.9794
Evaluate side-chains
  212 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 209
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0030
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
B 327 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.160161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.111787 restraints weight = 22085.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.115383 restraints weight = 14297.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.117847 restraints weight = 10491.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.119534 restraints weight = 8397.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.120774 restraints weight = 7159.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.4560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9551  Z= 0.139
  Angle     :  0.558   6.122  12856  Z= 0.320
  Chirality :  0.042   0.159   1394
  Planarity :  0.004   0.030   1576
  Dihedral  :  4.619  16.195   1212
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.83 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.25), residues: 1104
  helix:  1.02 (0.20), residues: 592
  sheet:  0.11 (0.48), residues: 126
  loop : -0.31 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  23 
 TYR   0.025   0.002   TYR B 203 
 PHE   0.024   0.002   PHE B  22 
 TRP   0.017   0.002   TRP A 424 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9546)
  covalent geometry    : angle       0.55775 (12856)
  hydrogen bonds       : bond        0.05225 (  489)
  hydrogen bonds       : angle       5.28231 ( 1401)
  metal coordination   : bond        0.00086 (    4)
  Misc. bond           : bond        0.01022 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 281
  time to evaluate  : 0.271 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7318 (mppt)
REVERT: A  142 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8811 (mt-10)
REVERT: A  173 PHE cc_start: 0.6227 (m-80) cc_final: 0.5242 (m-80)
REVERT: A  181 LEU cc_start: 0.8440 (tp) cc_final: 0.8217 (tp)
REVERT: A  195 LEU cc_start: 0.8025 (mm) cc_final: 0.7760 (mm)
REVERT: A  213 HIS cc_start: 0.8824 (m-70) cc_final: 0.8314 (m90)
REVERT: A  247 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7125 (mtp-110)
REVERT: A  263 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: A  310 ILE cc_start: 0.8781 (mt) cc_final: 0.8564 (tp)
REVERT: A  316 ILE cc_start: 0.8479 (tp) cc_final: 0.8274 (tp)
REVERT: A  365 MET cc_start: 0.7402 (tmm) cc_final: 0.5927 (tmm)
REVERT: A  434 MET cc_start: 0.6768 (tpp) cc_final: 0.5873 (tpp)
REVERT: A  486 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6050 (mm-30)
REVERT: B    1 MET cc_start: 0.7517 (mmp) cc_final: 0.7272 (tpt)
REVERT: B   14 PHE cc_start: 0.7847 (t80) cc_final: 0.7619 (t80)
REVERT: B  142 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8923 (mt-10)
REVERT: B  152 ASN cc_start: 0.8131 (t0) cc_final: 0.7849 (m-40)
REVERT: B  173 PHE cc_start: 0.6220 (m-80) cc_final: 0.5196 (m-80)
REVERT: B  195 LEU cc_start: 0.8088 (mm) cc_final: 0.7583 (mm)
REVERT: B  213 HIS cc_start: 0.8841 (m-70) cc_final: 0.8321 (m90)
REVERT: B  247 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7244 (mtp180)
REVERT: B  310 ILE cc_start: 0.8839 (mt) cc_final: 0.8419 (tp)
REVERT: B  316 ILE cc_start: 0.8549 (tp) cc_final: 0.8347 (tp)
REVERT: B  365 MET cc_start: 0.7399 (tmm) cc_final: 0.5923 (tmm)
REVERT: B  434 MET cc_start: 0.6753 (tpp) cc_final: 0.5843 (tpp)
REVERT: B  486 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6087 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 282
  average time/residue: 0.0702
  time to fit residues: 29.1219
Evaluate side-chains
  211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 210
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 43 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 34 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
B 327 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.155638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.108174 restraints weight = 22692.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.111686 restraints weight = 14552.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.114168 restraints weight = 10633.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.115938 restraints weight = 8395.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.117125 restraints weight = 7042.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9551  Z= 0.133
  Angle     :  0.545   5.725  12856  Z= 0.306
  Chirality :  0.043   0.201   1394
  Planarity :  0.004   0.038   1576
  Dihedral  :  4.482  14.698   1212
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.25), residues: 1104
  helix:  1.05 (0.20), residues: 594
  sheet:  0.15 (0.48), residues: 126
  loop : -0.29 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  23 
 TYR   0.019   0.002   TYR B 203 
 PHE   0.023   0.002   PHE B 217 
 TRP   0.024   0.002   TRP B 475 
 HIS   0.006   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9546)
  covalent geometry    : angle       0.54524 (12856)
  hydrogen bonds       : bond        0.04721 (  489)
  hydrogen bonds       : angle       5.13936 ( 1401)
  metal coordination   : bond        0.00195 (    4)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8710 (t80) cc_final: 0.8470 (t80)
REVERT: A  142 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8743 (mt-10)
REVERT: A  195 LEU cc_start: 0.8098 (mm) cc_final: 0.7882 (mm)
REVERT: A  213 HIS cc_start: 0.8760 (m-70) cc_final: 0.8230 (m90)
REVERT: A  229 LEU cc_start: 0.8324 (mt) cc_final: 0.8009 (tp)
REVERT: A  247 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7555 (mtp85)
REVERT: A  263 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7427 (mt-10)
REVERT: A  267 ASP cc_start: 0.7632 (m-30) cc_final: 0.7343 (m-30)
REVERT: A  309 LEU cc_start: 0.8248 (mt) cc_final: 0.7827 (pp)
REVERT: A  310 ILE cc_start: 0.8793 (mt) cc_final: 0.8091 (tt)
REVERT: A  434 MET cc_start: 0.6819 (tpp) cc_final: 0.5924 (tpp)
REVERT: A  486 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6088 (mm-30)
REVERT: B    1 MET cc_start: 0.7476 (mmp) cc_final: 0.7262 (tpt)
REVERT: B   12 PHE cc_start: 0.8711 (t80) cc_final: 0.8499 (t80)
REVERT: B   37 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7344 (mmtm)
REVERT: B   43 LEU cc_start: 0.8881 (mt) cc_final: 0.8677 (mt)
REVERT: B  195 LEU cc_start: 0.8101 (mm) cc_final: 0.7831 (mm)
REVERT: B  213 HIS cc_start: 0.8730 (m-70) cc_final: 0.8239 (m90)
REVERT: B  229 LEU cc_start: 0.8315 (mt) cc_final: 0.8021 (tp)
REVERT: B  247 ARG cc_start: 0.7740 (mtp85) cc_final: 0.7517 (mtp180)
REVERT: B  309 LEU cc_start: 0.8492 (mt) cc_final: 0.7821 (pp)
REVERT: B  310 ILE cc_start: 0.8874 (mt) cc_final: 0.8377 (tp)
REVERT: B  434 MET cc_start: 0.6799 (tpp) cc_final: 0.5914 (tpp)
REVERT: B  486 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6062 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.0648
  time to fit residues: 25.0905
Evaluate side-chains
  210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 51 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 67 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 278 ASN
A 327 GLN
A 537 ASN
B 134 GLN
** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 278 ASN
B 327 GLN
B 537 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.148219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.102725 restraints weight = 23793.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.105863 restraints weight = 15914.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.108009 restraints weight = 11875.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.109504 restraints weight = 9627.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.110451 restraints weight = 8254.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.5731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9551  Z= 0.234
  Angle     :  0.661   7.426  12856  Z= 0.364
  Chirality :  0.045   0.164   1394
  Planarity :  0.004   0.044   1576
  Dihedral  :  4.964  18.079   1212
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.24), residues: 1104
  helix:  0.40 (0.20), residues: 596
  sheet: -0.12 (0.49), residues: 130
  loop : -0.74 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 235 
 TYR   0.016   0.002   TYR B 441 
 PHE   0.021   0.002   PHE A 119 
 TRP   0.011   0.002   TRP B 475 
 HIS   0.011   0.002   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 9546)
  covalent geometry    : angle       0.66111 (12856)
  hydrogen bonds       : bond        0.05220 (  489)
  hydrogen bonds       : angle       5.49856 ( 1401)
  metal coordination   : bond        0.00616 (    4)
  Misc. bond           : bond        0.00622 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8770 (mt-10)
REVERT: A  213 HIS cc_start: 0.8765 (m-70) cc_final: 0.8217 (m90)
REVERT: A  278 ASN cc_start: 0.7058 (t0) cc_final: 0.6779 (t0)
REVERT: A  309 LEU cc_start: 0.8413 (mt) cc_final: 0.7930 (pp)
REVERT: A  310 ILE cc_start: 0.8966 (mt) cc_final: 0.8288 (tt)
REVERT: A  327 GLN cc_start: 0.5446 (tm130) cc_final: 0.5097 (tm-30)
REVERT: A  328 PHE cc_start: 0.6887 (m-80) cc_final: 0.6411 (m-80)
REVERT: A  486 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6143 (mm-30)
REVERT: B    1 MET cc_start: 0.7784 (mmp) cc_final: 0.7423 (tpt)
REVERT: B   37 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7483 (mmtm)
REVERT: B  142 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8777 (mt-10)
REVERT: B  171 ILE cc_start: 0.9335 (mm) cc_final: 0.8983 (tp)
REVERT: B  195 LEU cc_start: 0.8288 (mm) cc_final: 0.8069 (mm)
REVERT: B  213 HIS cc_start: 0.8756 (m-70) cc_final: 0.8215 (m90)
REVERT: B  278 ASN cc_start: 0.7045 (t0) cc_final: 0.6785 (t0)
REVERT: B  310 ILE cc_start: 0.9047 (mt) cc_final: 0.8658 (tt)
REVERT: B  486 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6115 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0676
  time to fit residues: 22.7483
Evaluate side-chains
  191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 95 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0970
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 99 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
A 327 GLN
A 428 GLN
B 227 ASN
B 327 GLN
B 428 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.153956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.107306 restraints weight = 22811.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.110480 restraints weight = 15205.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.112775 restraints weight = 11402.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.114106 restraints weight = 9226.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.115417 restraints weight = 7957.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6631
moved from start:          0.6069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9551  Z= 0.119
  Angle     :  0.548  10.085  12856  Z= 0.301
  Chirality :  0.042   0.155   1394
  Planarity :  0.004   0.047   1576
  Dihedral  :  4.609  16.353   1212
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.25), residues: 1104
  helix:  0.59 (0.20), residues: 600
  sheet: -0.15 (0.49), residues: 130
  loop : -0.47 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 294 
 TYR   0.020   0.001   TYR B 203 
 PHE   0.025   0.002   PHE B 217 
 TRP   0.029   0.002   TRP B 475 
 HIS   0.006   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9546)
  covalent geometry    : angle       0.54788 (12856)
  hydrogen bonds       : bond        0.04313 (  489)
  hydrogen bonds       : angle       5.17505 ( 1401)
  metal coordination   : bond        0.00139 (    4)
  Misc. bond           : bond        0.00481 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 MET cc_start: 0.6846 (mtt) cc_final: 0.6319 (mtt)
REVERT: A   37 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7357 (mppt)
REVERT: A   43 LEU cc_start: 0.8959 (mt) cc_final: 0.8686 (mt)
REVERT: A  142 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8832 (mt-10)
REVERT: A  171 ILE cc_start: 0.9312 (mm) cc_final: 0.9012 (tp)
REVERT: A  195 LEU cc_start: 0.8271 (mm) cc_final: 0.7907 (mm)
REVERT: A  213 HIS cc_start: 0.8751 (m-70) cc_final: 0.8211 (m90)
REVERT: A  247 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7287 (mtp180)
REVERT: A  263 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7923 (mt-10)
REVERT: A  309 LEU cc_start: 0.8272 (mt) cc_final: 0.7789 (pp)
REVERT: A  310 ILE cc_start: 0.8838 (mt) cc_final: 0.8404 (tt)
REVERT: A  311 LEU cc_start: 0.8397 (mt) cc_final: 0.8114 (pp)
REVERT: A  486 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6064 (mm-30)
REVERT: B    1 MET cc_start: 0.7623 (mmp) cc_final: 0.6807 (tmm)
REVERT: B    5 LEU cc_start: 0.8710 (mt) cc_final: 0.8381 (mt)
REVERT: B   37 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7596 (mmtm)
REVERT: B   43 LEU cc_start: 0.8969 (mt) cc_final: 0.8703 (mt)
REVERT: B  142 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8886 (mt-10)
REVERT: B  171 ILE cc_start: 0.9299 (mm) cc_final: 0.9045 (tp)
REVERT: B  195 LEU cc_start: 0.8279 (mm) cc_final: 0.7875 (mm)
REVERT: B  213 HIS cc_start: 0.8795 (m-70) cc_final: 0.8223 (m90)
REVERT: B  247 ARG cc_start: 0.7487 (mmm160) cc_final: 0.7231 (mmm160)
REVERT: B  263 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7631 (mm-30)
REVERT: B  310 ILE cc_start: 0.8770 (mt) cc_final: 0.8535 (tt)
REVERT: B  328 PHE cc_start: 0.6585 (m-80) cc_final: 0.6331 (m-80)
REVERT: B  486 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6058 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.0797
  time to fit residues: 30.8684
Evaluate side-chains
  206 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 227 ASN
A 252 ASN
A 278 ASN
A 327 GLN
** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.155756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.108438 restraints weight = 23040.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.112003 restraints weight = 14821.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.114418 restraints weight = 10803.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.116069 restraints weight = 8598.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.117218 restraints weight = 7291.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.6327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9551  Z= 0.133
  Angle     :  0.586  14.177  12856  Z= 0.319
  Chirality :  0.043   0.178   1394
  Planarity :  0.004   0.046   1576
  Dihedral  :  4.555  23.048   1212
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.25), residues: 1104
  helix:  0.65 (0.20), residues: 600
  sheet:  0.16 (0.50), residues: 130
  loop : -0.49 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 444 
 TYR   0.017   0.001   TYR B 203 
 PHE   0.026   0.002   PHE B 217 
 TRP   0.016   0.001   TRP B 424 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9546)
  covalent geometry    : angle       0.58628 (12856)
  hydrogen bonds       : bond        0.04441 (  489)
  hydrogen bonds       : angle       5.19852 ( 1401)
  metal coordination   : bond        0.00236 (    4)
  Misc. bond           : bond        0.00848 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9301 (mm) cc_final: 0.9081 (mm)
REVERT: A   22 PHE cc_start: 0.8525 (m-10) cc_final: 0.8124 (m-80)
REVERT: A   43 LEU cc_start: 0.8861 (mt) cc_final: 0.8550 (mt)
REVERT: A  142 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8812 (mt-10)
REVERT: A  171 ILE cc_start: 0.9292 (mm) cc_final: 0.9012 (tp)
REVERT: A  173 PHE cc_start: 0.6327 (m-80) cc_final: 0.5975 (m-80)
REVERT: A  195 LEU cc_start: 0.8216 (mm) cc_final: 0.7961 (mm)
REVERT: A  213 HIS cc_start: 0.8711 (m-70) cc_final: 0.8113 (m90)
REVERT: A  247 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7287 (mtp180)
REVERT: A  267 ASP cc_start: 0.8080 (m-30) cc_final: 0.7862 (m-30)
REVERT: A  309 LEU cc_start: 0.8297 (mt) cc_final: 0.7747 (pp)
REVERT: A  310 ILE cc_start: 0.8754 (mt) cc_final: 0.8279 (tt)
REVERT: A  322 MET cc_start: 0.8862 (ttm) cc_final: 0.8659 (ttm)
REVERT: A  368 MET cc_start: 0.7495 (ppp) cc_final: 0.7232 (ppp)
REVERT: A  434 MET cc_start: 0.6982 (tpp) cc_final: 0.6178 (tpp)
REVERT: A  486 GLU cc_start: 0.6523 (mt-10) cc_final: 0.5778 (mm-30)
REVERT: B    1 MET cc_start: 0.7598 (mmp) cc_final: 0.6791 (tmm)
REVERT: B    5 LEU cc_start: 0.8670 (mt) cc_final: 0.8399 (mt)
REVERT: B   15 ILE cc_start: 0.9281 (mm) cc_final: 0.9038 (mm)
REVERT: B   33 MET cc_start: 0.6622 (mpp) cc_final: 0.6250 (mpp)
REVERT: B   43 LEU cc_start: 0.8862 (mt) cc_final: 0.8554 (mt)
REVERT: B  130 TYR cc_start: 0.7554 (t80) cc_final: 0.7312 (t80)
REVERT: B  142 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8881 (mt-10)
REVERT: B  173 PHE cc_start: 0.6323 (m-80) cc_final: 0.5945 (m-80)
REVERT: B  195 LEU cc_start: 0.8210 (mm) cc_final: 0.7938 (mm)
REVERT: B  213 HIS cc_start: 0.8730 (m-70) cc_final: 0.8135 (m90)
REVERT: B  247 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6948 (mmm160)
REVERT: B  310 ILE cc_start: 0.8790 (mt) cc_final: 0.8579 (tt)
REVERT: B  368 MET cc_start: 0.7477 (ppp) cc_final: 0.7180 (ppp)
REVERT: B  486 GLU cc_start: 0.6591 (mt-10) cc_final: 0.5810 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0881
  time to fit residues: 31.0873
Evaluate side-chains
  199 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0870
   chunk 55 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 86 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.7162

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.156302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.109783 restraints weight = 23059.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.113401 restraints weight = 14651.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.115817 restraints weight = 10645.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.117495 restraints weight = 8441.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.118672 restraints weight = 7122.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.6600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9551  Z= 0.130
  Angle     :  0.612  19.948  12856  Z= 0.331
  Chirality :  0.044   0.205   1394
  Planarity :  0.004   0.049   1576
  Dihedral  :  4.557  17.581   1212
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.25), residues: 1104
  helix:  0.81 (0.20), residues: 594
  sheet:  0.24 (0.51), residues: 130
  loop : -0.57 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 194 
 TYR   0.018   0.001   TYR B 203 
 PHE   0.027   0.002   PHE A 121 
 TRP   0.023   0.002   TRP B 540 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9546)
  covalent geometry    : angle       0.61221 (12856)
  hydrogen bonds       : bond        0.04352 (  489)
  hydrogen bonds       : angle       5.31677 ( 1401)
  metal coordination   : bond        0.00157 (    4)
  Misc. bond           : bond        0.01348 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9266 (mm) cc_final: 0.9059 (mm)
REVERT: A   22 PHE cc_start: 0.8507 (m-10) cc_final: 0.7806 (m-80)
REVERT: A   37 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7321 (mppt)
REVERT: A  125 LEU cc_start: 0.9100 (tp) cc_final: 0.8839 (pp)
REVERT: A  142 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8821 (mt-10)
REVERT: A  173 PHE cc_start: 0.6458 (m-80) cc_final: 0.6029 (m-80)
REVERT: A  195 LEU cc_start: 0.8107 (mm) cc_final: 0.7864 (mm)
REVERT: A  213 HIS cc_start: 0.8707 (m-70) cc_final: 0.8119 (m90)
REVERT: A  247 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7330 (mtp180)
REVERT: A  263 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7614 (mt-10)
REVERT: A  309 LEU cc_start: 0.8322 (mt) cc_final: 0.7772 (pp)
REVERT: A  310 ILE cc_start: 0.8741 (mt) cc_final: 0.8235 (tt)
REVERT: A  368 MET cc_start: 0.7203 (ppp) cc_final: 0.6813 (ppp)
REVERT: A  434 MET cc_start: 0.6981 (tpp) cc_final: 0.6200 (tpp)
REVERT: A  486 GLU cc_start: 0.6432 (mt-10) cc_final: 0.5666 (mm-30)
REVERT: B    1 MET cc_start: 0.7024 (mmp) cc_final: 0.6445 (tmm)
REVERT: B    5 LEU cc_start: 0.8597 (mt) cc_final: 0.8343 (mt)
REVERT: B   15 ILE cc_start: 0.9273 (mm) cc_final: 0.9028 (mm)
REVERT: B   43 LEU cc_start: 0.8799 (mt) cc_final: 0.8552 (mt)
REVERT: B  125 LEU cc_start: 0.9127 (tp) cc_final: 0.8871 (pp)
REVERT: B  213 HIS cc_start: 0.8756 (m-70) cc_final: 0.8120 (m90)
REVERT: B  247 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6918 (mmm160)
REVERT: B  264 SER cc_start: 0.8538 (p) cc_final: 0.8090 (p)
REVERT: B  310 ILE cc_start: 0.8721 (mt) cc_final: 0.8513 (tt)
REVERT: B  368 MET cc_start: 0.7328 (ppp) cc_final: 0.6906 (ppp)
REVERT: B  486 GLU cc_start: 0.6420 (mt-10) cc_final: 0.5666 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.0882
  time to fit residues: 31.2251
Evaluate side-chains
  192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0670
   chunk 24 optimal weight:    0.2980
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   overall best weight:    1.0522

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 327 GLN
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.155792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.108659 restraints weight = 23144.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.112102 restraints weight = 14961.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.114519 restraints weight = 11016.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.116028 restraints weight = 8815.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.117226 restraints weight = 7555.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.6787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9551  Z= 0.141
  Angle     :  0.616  13.920  12856  Z= 0.338
  Chirality :  0.044   0.165   1394
  Planarity :  0.004   0.048   1576
  Dihedral  :  4.525  16.780   1212
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.25), residues: 1104
  helix:  0.94 (0.20), residues: 580
  sheet:  0.34 (0.50), residues: 130
  loop : -0.44 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 194 
 TYR   0.016   0.001   TYR B 203 
 PHE   0.026   0.002   PHE B 217 
 TRP   0.014   0.001   TRP B 424 
 HIS   0.005   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9546)
  covalent geometry    : angle       0.61551 (12856)
  hydrogen bonds       : bond        0.04577 (  489)
  hydrogen bonds       : angle       5.33946 ( 1401)
  metal coordination   : bond        0.00267 (    4)
  Misc. bond           : bond        0.00984 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.8864 (mt) cc_final: 0.8519 (mt)
REVERT: A  202 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: A  213 HIS cc_start: 0.8744 (m-70) cc_final: 0.8094 (m90)
REVERT: A  263 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7429 (mp0)
REVERT: A  309 LEU cc_start: 0.8369 (mt) cc_final: 0.7818 (pp)
REVERT: A  310 ILE cc_start: 0.8740 (mt) cc_final: 0.8237 (tt)
REVERT: A  368 MET cc_start: 0.7269 (ppp) cc_final: 0.6870 (ppp)
REVERT: A  434 MET cc_start: 0.6995 (tpp) cc_final: 0.6231 (tpp)
REVERT: A  486 GLU cc_start: 0.6070 (mt-10) cc_final: 0.5369 (mm-30)
REVERT: B    1 MET cc_start: 0.7028 (mmp) cc_final: 0.6582 (tmm)
REVERT: B   15 ILE cc_start: 0.9294 (mm) cc_final: 0.9040 (mm)
REVERT: B   43 LEU cc_start: 0.8905 (mt) cc_final: 0.8584 (mt)
REVERT: B  213 HIS cc_start: 0.8787 (m-70) cc_final: 0.8100 (m90)
REVERT: B  263 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8050 (mm-30)
REVERT: B  310 ILE cc_start: 0.8778 (mt) cc_final: 0.8574 (tt)
REVERT: B  368 MET cc_start: 0.7375 (ppp) cc_final: 0.6985 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.0862
  time to fit residues: 29.0714
Evaluate side-chains
  190 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.155948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.108727 restraints weight = 23470.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.112293 restraints weight = 15105.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.114634 restraints weight = 11059.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.116311 restraints weight = 8874.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.117502 restraints weight = 7559.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.7008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9551  Z= 0.149
  Angle     :  0.639  18.433  12856  Z= 0.348
  Chirality :  0.044   0.209   1394
  Planarity :  0.004   0.047   1576
  Dihedral  :  4.529  17.090   1212
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.25), residues: 1104
  helix:  0.75 (0.20), residues: 594
  sheet:  0.30 (0.51), residues: 130
  loop : -0.45 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 194 
 TYR   0.014   0.002   TYR B 203 
 PHE   0.031   0.002   PHE B  21 
 TRP   0.014   0.001   TRP A 424 
 HIS   0.005   0.001   HIS B 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9546)
  covalent geometry    : angle       0.63870 (12856)
  hydrogen bonds       : bond        0.04688 (  489)
  hydrogen bonds       : angle       5.49307 ( 1401)
  metal coordination   : bond        0.00412 (    4)
  Misc. bond           : bond        0.01557 (    1)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ILE cc_start: 0.9255 (mm) cc_final: 0.8910 (mm)
REVERT: A   43 LEU cc_start: 0.8762 (mt) cc_final: 0.8523 (mt)
REVERT: A  195 LEU cc_start: 0.8086 (mm) cc_final: 0.7852 (mm)
REVERT: A  213 HIS cc_start: 0.8731 (m-70) cc_final: 0.8118 (m90)
REVERT: A  263 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7521 (mp0)
REVERT: A  309 LEU cc_start: 0.8360 (mt) cc_final: 0.7805 (pp)
REVERT: A  310 ILE cc_start: 0.8703 (mt) cc_final: 0.8193 (tt)
REVERT: A  363 PHE cc_start: 0.6993 (t80) cc_final: 0.6623 (t80)
REVERT: A  368 MET cc_start: 0.7421 (ppp) cc_final: 0.7025 (ppp)
REVERT: A  434 MET cc_start: 0.6932 (tpp) cc_final: 0.6161 (ppp)
REVERT: B    1 MET cc_start: 0.7019 (mmp) cc_final: 0.6754 (tpt)
REVERT: B   15 ILE cc_start: 0.9260 (mm) cc_final: 0.8830 (mm)
REVERT: B   43 LEU cc_start: 0.8823 (mt) cc_final: 0.8507 (mt)
REVERT: B  213 HIS cc_start: 0.8759 (m-70) cc_final: 0.8155 (m90)
REVERT: B  263 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8059 (mm-30)
REVERT: B  368 MET cc_start: 0.7452 (ppp) cc_final: 0.7069 (ppp)
REVERT: B  569 GLU cc_start: 0.7800 (pt0) cc_final: 0.7317 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.0843
  time to fit residues: 29.4448
Evaluate side-chains
  184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    0.0010
   chunk 94 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 102 optimal weight:    8.9990
   chunk 2 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0980
   chunk 96 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 327 GLN
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 567 ASN
B 327 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.157337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.111024 restraints weight = 22542.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.114555 restraints weight = 14645.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.116901 restraints weight = 10736.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.118541 restraints weight = 8590.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.119666 restraints weight = 7299.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.7213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9551  Z= 0.128
  Angle     :  0.630  18.968  12856  Z= 0.341
  Chirality :  0.044   0.190   1394
  Planarity :  0.004   0.048   1576
  Dihedral  :  4.416  16.160   1212
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.25), residues: 1104
  helix:  0.97 (0.21), residues: 582
  sheet:  0.19 (0.50), residues: 130
  loop : -0.36 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 247 
 TYR   0.035   0.001   TYR A 203 
 PHE   0.029   0.002   PHE A 217 
 TRP   0.016   0.001   TRP A 424 
 HIS   0.005   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9546)
  covalent geometry    : angle       0.62977 (12856)
  hydrogen bonds       : bond        0.04456 (  489)
  hydrogen bonds       : angle       5.35468 ( 1401)
  metal coordination   : bond        0.00182 (    4)
  Misc. bond           : bond        0.01412 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1658.68 seconds
wall clock time: 29 minutes 36.85 seconds (1776.85 seconds total)