Starting phenix.real_space_refine
on Sat Aug 23 00:28:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8phf_17660/08_2025/8phf_17660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8phf_17660/08_2025/8phf_17660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8phf_17660/08_2025/8phf_17660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8phf_17660/08_2025/8phf_17660.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8phf_17660/08_2025/8phf_17660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8phf_17660/08_2025/8phf_17660.map"
  }
  resolution = 3.6
  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=   0.004 sd=   0.103
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
     P       4      5.49       5
     S      44      5.16       5
     C    5488      2.51       5
     N    1462      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 8640
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4267
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 15, 'TRANS': 531}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4267
          Classifications: {'peptide': 547}
          Link IDs: {'PTRANS': 15, 'TRANS': 531}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.48, per 1000 atoms: 0.29
  Number of scatterers: 8640
  At special positions: 0
  Unit cell: (121.8, 98.28, 76.44, 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)
     S      44     16.00
     P       4     15.00
     O    1642      8.00
     N    1462      7.00
     C    5488      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: 0.87
  Conformation dependent library (CDL) restraints added in 334.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      63.2% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 54
      removed outlier: 3.673A  pdb=" N   VAL A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 81
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 112 through 116
      removed outlier: 3.543A  pdb=" N   GLY A 116 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 133
      removed outlier: 3.519A  pdb=" N   ILE A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 147
      removed outlier: 3.999A  pdb=" N   VAL A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 157
      removed outlier: 3.565A  pdb=" N   ILE A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 172
      Proline residue:  A 167  - end of helix
    Processing helix  chain 'A' and resid 188 through 192
      removed outlier: 3.548A  pdb=" N   ILE A 192 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 252
      No H-bonds generated for 'chain 'A' and resid 250 through 252'
    Processing helix  chain 'A' and resid 291 through 301
    Processing helix  chain 'A' and resid 305 through 326
      removed outlier: 3.824A  pdb=" N   SER A 309 " --> pdb=" O   PHE A 305 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   VAL A 311 " --> pdb=" O   MET A 307 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ALA A 312 " --> pdb=" O   GLY A 308 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ARG A 317 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   TYR A 325 " --> pdb=" O   MET A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 368
    Processing helix  chain 'A' and resid 375 through 402
      removed outlier: 3.762A  pdb=" N   ALA A 379 " --> pdb=" O   CYS A 375 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 405
      No H-bonds generated for 'chain 'A' and resid 403 through 405'
    Processing helix  chain 'A' and resid 411 through 420
      removed outlier: 3.915A  pdb=" N   ARG A 420 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 424
    Processing helix  chain 'A' and resid 431 through 449
      removed outlier: 3.831A  pdb=" N   TYR A 435 " --> pdb=" O   ILE A 431 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE A 436 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ALA A 437 " --> pdb=" O   ARG A 433 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   GLY A 440 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   HIS A 443 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 447 " --> pdb=" O   HIS A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 493
      No H-bonds generated for 'chain 'A' and resid 491 through 493'
    Processing helix  chain 'A' and resid 494 through 519
      removed outlier: 3.594A  pdb=" N   ALA A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU A 503 " --> pdb=" O   ASN A 499 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   PHE A 508 " --> pdb=" O   ASN A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 525
      removed outlier: 4.471A  pdb=" N   MET A 524 " --> pdb=" O   LYS A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 557
      removed outlier: 3.580A  pdb=" N   LEU A 530 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.550A  pdb=" N   GLN A 585 " --> pdb=" O   PHE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 609
    Processing helix  chain 'B' and resid 39 through 43
    Processing helix  chain 'B' and resid 60 through 81
      removed outlier: 3.597A  pdb=" N   LEU B  64 " --> pdb=" O   SER B  60 " (cutoff:3.500A)
      Proline residue:  B  73  - end of helix
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 94 through 105
    Processing helix  chain 'B' and resid 106 through 109
      removed outlier: 3.769A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 106 through 109'
    Processing helix  chain 'B' and resid 112 through 116
    Processing helix  chain 'B' and resid 121 through 133
      removed outlier: 3.983A  pdb=" N   ILE B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 147
      removed outlier: 3.555A  pdb=" N   THR B 141 " --> pdb=" O   SER B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 157
      removed outlier: 3.546A  pdb=" N   ILE B 154 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 171
      Proline residue:  B 167  - end of helix
    Processing helix  chain 'B' and resid 291 through 302
      removed outlier: 4.133A  pdb=" N   VAL B 295 " --> pdb=" O   ASP B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 320
      removed outlier: 3.916A  pdb=" N   SER B 309 " --> pdb=" O   PHE B 305 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA B 312 " --> pdb=" O   GLY B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 329
      removed outlier: 3.608A  pdb=" N   TYR B 325 " --> pdb=" O   MET B 321 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   CYS B 327 " --> pdb=" O   ALA B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 367
      removed outlier: 4.127A  pdb=" N   LYS B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 401
      removed outlier: 3.614A  pdb=" N   ALA B 379 " --> pdb=" O   CYS B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 407
      removed outlier: 3.503A  pdb=" N   TYR B 406 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR B 407 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 425
      removed outlier: 3.528A  pdb=" N   ILE B 415 " --> pdb=" O   PRO B 411 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG B 420 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ILE B 421 " --> pdb=" O   ARG B 417 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LEU B 422 " --> pdb=" O   ASP B 418 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU B 423 " --> pdb=" O   THR B 419 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE B 424 " --> pdb=" O   ARG B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 449
      removed outlier: 3.630A  pdb=" N   ALA B 437 " --> pdb=" O   ARG B 433 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLY B 440 " --> pdb=" O   ILE B 436 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE B 447 " --> pdb=" O   HIS B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 493
      No H-bonds generated for 'chain 'B' and resid 491 through 493'
    Processing helix  chain 'B' and resid 494 through 520
    Processing helix  chain 'B' and resid 521 through 525
      removed outlier: 4.369A  pdb=" N   MET B 524 " --> pdb=" O   LYS B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 557
      removed outlier: 3.690A  pdb=" N   LYS B 531 " --> pdb=" O   GLN B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.589A  pdb=" N   PHE B 571 " --> pdb=" O   LEU B 567 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN B 585 " --> pdb=" O   PHE B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 609
    Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 177
    Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 198
      removed outlier: 6.489A  pdb=" N   TYR A 205 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LYS A 279 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   LEU A 207 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A 273 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   TRP A 213 " --> pdb=" O   CYS A 271 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   CYS A 271 " --> pdb=" O   TRP A 213 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331
    Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 177
      removed outlier: 7.464A  pdb=" N   ALA B 177 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   PHE B 226 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 195 through 198
      removed outlier: 6.560A  pdb=" N   TYR B 205 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   LYS B 279 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   LEU B 207 " --> pdb=" O   ASN B 277 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   TRP B 213 " --> pdb=" O   CYS B 271 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   CYS B 271 " --> pdb=" O   TRP B 213 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 330 through 331

    483 hydrogen bonds defined for protein.
    1407 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: 1.39

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2141
        1.33 -     1.45: 1616
        1.45 -     1.57: 4959
        1.57 -     1.69: 6
        1.69 -     1.81: 70
  Bond restraints: 8792
  Sorted by residual:
  bond pdb=" O3P FAD A 701 "
       pdb=" P   FAD A 701 "
    ideal  model  delta    sigma   weight residual
    1.660  1.582  0.078 2.00e-02 2.50e+03 1.52e+01
  bond pdb=" O3P FAD B 701 "
       pdb=" P   FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.660  1.586  0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" O5B FAD B 701 "
       pdb=" PA  FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.634  1.567  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" O5B FAD A 701 "
       pdb=" PA  FAD A 701 "
    ideal  model  delta    sigma   weight residual
    1.634  1.570  0.064 2.00e-02 2.50e+03 1.01e+01
  bond pdb=" O5' FAD B 701 "
       pdb=" P   FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.637  1.574  0.063 2.00e-02 2.50e+03 9.94e+00
  ... (remaining 8787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 11536
        1.64 -     3.28: 271
        3.28 -     4.92: 37
        4.92 -     6.56: 13
        6.56 -     8.20: 11
  Bond angle restraints: 11868
  Sorted by residual:
  angle pdb=" CA  GLU A 426 "
        pdb=" CB  GLU A 426 "
        pdb=" CG  GLU A 426 "
      ideal   model   delta    sigma   weight residual
     114.10  120.00   -5.90 2.00e+00 2.50e-01 8.70e+00
  angle pdb=" N   GLY A 186 "
        pdb=" CA  GLY A 186 "
        pdb=" C   GLY A 186 "
      ideal   model   delta    sigma   weight residual
     113.18  106.51    6.67 2.37e+00 1.78e-01 7.93e+00
  angle pdb=" CB  MET B 124 "
        pdb=" CG  MET B 124 "
        pdb=" SD  MET B 124 "
      ideal   model   delta    sigma   weight residual
     112.70  104.50    8.20 3.00e+00 1.11e-01 7.47e+00
  angle pdb=" P   FAD A 701 "
        pdb=" O3P FAD A 701 "
        pdb=" PA  FAD A 701 "
      ideal   model   delta    sigma   weight residual
     130.34  122.41    7.93 3.00e+00 1.11e-01 6.99e+00
  angle pdb=" CB  MET B 356 "
        pdb=" CG  MET B 356 "
        pdb=" SD  MET B 356 "
      ideal   model   delta    sigma   weight residual
     112.70  104.81    7.89 3.00e+00 1.11e-01 6.91e+00
  ... (remaining 11863 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.99: 5159
       32.99 -    65.97: 150
       65.97 -    98.96: 33
       98.96 -   131.94: 0
      131.94 -   164.93: 2
  Dihedral angle restraints: 5344
    sinusoidal: 2210
      harmonic: 3134
  Sorted by residual:
  dihedral pdb=" O5' FAD A 701 "
           pdb=" O3P FAD A 701 "
           pdb=" P   FAD A 701 "
           pdb=" PA  FAD A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.23  133.30  164.93     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" CA  PHE A 425 "
           pdb=" C   PHE A 425 "
           pdb=" N   GLU A 426 "
           pdb=" CA  GLU A 426 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.52  -21.48     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" O5' FAD B 701 "
           pdb=" O3P FAD B 701 "
           pdb=" P   FAD B 701 "
           pdb=" PA  FAD B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.23  163.59  134.64     1      3.00e+01 1.11e-03 1.82e+01
  ... (remaining 5341 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 955
       0.042 -    0.084: 312
       0.084 -    0.125: 67
       0.125 -    0.167: 7
       0.167 -    0.209: 3
  Chirality restraints: 1344
  Sorted by residual:
  chirality pdb=" C2B FAD B 701 "
            pdb=" C1B FAD B 701 "
            pdb=" C3B FAD B 701 "
            pdb=" O2B FAD B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.74    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ARG B 329 "
            pdb=" N   ARG B 329 "
            pdb=" C   ARG B 329 "
            pdb=" CB  ARG B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  PHE A  54 "
            pdb=" N   PHE A  54 "
            pdb=" C   PHE A  54 "
            pdb=" CB  PHE A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.03e-01
  ... (remaining 1341 not shown)

  Planarity restraints: 1506
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 182 "   -0.030 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO B 183 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 183 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 183 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 425 "    0.009 2.00e-02 2.50e+03   1.35e-02 3.19e+00
        pdb=" CG  PHE A 425 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 425 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 425 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 425 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 425 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 425 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 515 "   -0.008 2.00e-02 2.50e+03   1.50e-02 2.26e+00
        pdb=" C   LEU A 515 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A 515 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 516 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1503 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 139
        2.69 -     3.24: 8786
        3.24 -     3.79: 13185
        3.79 -     4.35: 17375
        4.35 -     4.90: 28706
  Nonbonded interactions: 68191
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  64 "
            pdb=" ND2 ASN A  68 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG  SER B  60 "
            pdb=" OE1 GLU B  63 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG  SER A  60 "
            pdb=" OD1 ASP A  62 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O3' FAD B 701 "
            pdb=" O5' FAD B 701 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OD2 ASP A 201 "
            pdb=" NZ  LYS A 203 "
     model   vdw
     2.261 3.120
  ... (remaining 68186 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.830
  Find NCS groups from input model:        0.130
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
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      :  0.004   0.078   8793  Z= 0.214
  Angle     :  0.651   8.201  11868  Z= 0.327
  Chirality :  0.042   0.209   1344
  Planarity :  0.004   0.045   1506
  Dihedral  : 16.415 164.926   3332
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.33 %
    Favored  : 99.57 %
  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:  0.67 (0.26), residues: 1086
  helix:  1.03 (0.21), residues: 596
  sheet: -1.02 (0.53), residues: 90
  loop :  0.11 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 609 
 TYR   0.021   0.001   TYR B 361 
 PHE   0.031   0.002   PHE A 425 
 TRP   0.004   0.001   TRP B 213 
 HIS   0.007   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8792)
  covalent geometry    : angle       0.65059 (11868)
  hydrogen bonds       : bond        0.17305 (  483)
  hydrogen bonds       : angle       6.45148 ( 1407)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.7705 (m-30) cc_final: 0.7185 (m-30)
REVERT: A  609 ARG cc_start: 0.6539 (mmt180) cc_final: 0.6175 (tpt170)
REVERT: B  619 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.7123 (ttm-80)
  outliers start: 1
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1144
  time to fit residues: 19.0767
Evaluate side-chains
  93 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  327 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0170
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 122 ASN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 HIS
B 527 GLN
B 585 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.221709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.197270 restraints weight = 8443.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.199433 restraints weight = 8020.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.201090 restraints weight = 6192.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.202948 restraints weight = 5083.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.203541 restraints weight = 4438.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8793  Z= 0.125
  Angle     :  0.558   8.436  11868  Z= 0.285
  Chirality :  0.040   0.148   1344
  Planarity :  0.004   0.045   1506
  Dihedral  : 11.066 167.160   1267
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  6.41 %
    Favored  : 91.85 %
  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:  1.28 (0.26), residues: 1086
  helix:  1.56 (0.21), residues: 620
  sheet: -1.03 (0.53), residues: 84
  loop :  0.28 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 414 
 TYR   0.019   0.001   TYR A 361 
 PHE   0.013   0.001   PHE B 275 
 TRP   0.004   0.001   TRP A 213 
 HIS   0.007   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8792)
  covalent geometry    : angle       0.55759 (11868)
  hydrogen bonds       : bond        0.04790 (  483)
  hydrogen bonds       : angle       4.33799 ( 1407)
  Misc. bond           : bond        0.00070 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: B  619 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7110 (ttm-80)
  outliers start: 16
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1149
  time to fit residues: 17.6386
Evaluate side-chains
  103 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  585 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0570
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0870
   chunk 79 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 GLN
B 204 HIS
B 216 ASN
B 331 GLN
B 585 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.223055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.196683 restraints weight = 8406.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.200259 restraints weight = 6163.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.202382 restraints weight = 4926.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.204567 restraints weight = 4224.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.205560 restraints weight = 3748.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8793  Z= 0.114
  Angle     :  0.517   7.362  11868  Z= 0.265
  Chirality :  0.039   0.136   1344
  Planarity :  0.004   0.044   1506
  Dihedral  :  9.859 170.324   1267
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.65 %
    Favored  : 87.17 %
  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:  1.40 (0.26), residues: 1086
  helix:  1.72 (0.21), residues: 610
  sheet: -0.95 (0.51), residues: 90
  loop :  0.26 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 532 
 TYR   0.018   0.001   TYR A 361 
 PHE   0.009   0.001   PHE A 178 
 TRP   0.002   0.001   TRP A 391 
 HIS   0.002   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8792)
  covalent geometry    : angle       0.51677 (11868)
  hydrogen bonds       : bond        0.04326 (  483)
  hydrogen bonds       : angle       4.07313 ( 1407)
  Misc. bond           : bond        0.00083 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: B  357 GLU cc_start: 0.6368 (mm-30) cc_final: 0.5827 (mt-10)
REVERT: B  619 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.7116 (ttm-80)
  outliers start: 20
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1201
  time to fit residues: 19.0288
Evaluate side-chains
  109 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  584 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0870
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
A 504 ASN
** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.214143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.186573 restraints weight = 8657.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.189198 restraints weight = 9209.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.191912 restraints weight = 6657.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.192519 restraints weight = 5276.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.193035 restraints weight = 4736.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8793  Z= 0.168
  Angle     :  0.575   7.505  11868  Z= 0.296
  Chirality :  0.041   0.136   1344
  Planarity :  0.004   0.043   1506
  Dihedral  :  9.818 174.966   1266
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.72 %
    Favored  : 84.24 %
  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:  1.02 (0.26), residues: 1086
  helix:  1.37 (0.21), residues: 616
  sheet: -1.18 (0.52), residues: 84
  loop :  0.15 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 335 
 TYR   0.019   0.001   TYR A 361 
 PHE   0.015   0.002   PHE B  44 
 TRP   0.005   0.001   TRP B 213 
 HIS   0.005   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 8792)
  covalent geometry    : angle       0.57545 (11868)
  hydrogen bonds       : bond        0.05116 (  483)
  hydrogen bonds       : angle       4.18485 ( 1407)
  Misc. bond           : bond        0.00055 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6352 (tt)
REVERT: B  357 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6273 (tt0)
REVERT: B  619 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7152 (ttm-80)
  outliers start: 28
  outliers final: 19
  residues processed: 117
  average time/residue: 0.1189
  time to fit residues: 18.6142
Evaluate side-chains
  112 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 105 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 ASN
** B 585 GLN ** 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 = 0.4450 r_free = 0.4450 target = 0.211415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.184542 restraints weight = 8663.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.187074 restraints weight = 8611.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.188250 restraints weight = 6749.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.188550 restraints weight = 5631.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.189285 restraints weight = 5284.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8793  Z= 0.188
  Angle     :  0.607   7.859  11868  Z= 0.314
  Chirality :  0.042   0.138   1344
  Planarity :  0.004   0.050   1506
  Dihedral  :  9.864 177.427   1266
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.80 %
    Favored  : 82.93 %
  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:  0.70 (0.26), residues: 1086
  helix:  1.13 (0.21), residues: 616
  sheet: -1.34 (0.51), residues: 90
  loop : -0.01 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 335 
 TYR   0.018   0.001   TYR A 361 
 PHE   0.019   0.002   PHE B  44 
 TRP   0.006   0.002   TRP B 213 
 HIS   0.006   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 8792)
  covalent geometry    : angle       0.60728 (11868)
  hydrogen bonds       : bond        0.05396 (  483)
  hydrogen bonds       : angle       4.27950 ( 1407)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6363 (tt)
REVERT: B  357 GLU cc_start: 0.6581 (mm-30) cc_final: 0.5640 (mt-10)
REVERT: B  619 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.7191 (ttm-80)
  outliers start: 30
  outliers final: 23
  residues processed: 112
  average time/residue: 0.1286
  time to fit residues: 18.9125
Evaluate side-chains
  113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  317 ARG
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 99 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:    0.3980
   chunk 16 optimal weight:    5.9990
   chunk 102 optimal weight:    0.4980
   chunk 107 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   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 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 585 GLN
B 204 HIS
** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.219519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.192808 restraints weight = 8481.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.196336 restraints weight = 6250.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.198447 restraints weight = 5051.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.200510 restraints weight = 4353.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.201474 restraints weight = 3876.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.4382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8793  Z= 0.114
  Angle     :  0.517   9.507  11868  Z= 0.267
  Chirality :  0.039   0.138   1344
  Planarity :  0.004   0.049   1506
  Dihedral  :  9.568 179.056   1266
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.00 %
    Favored  : 82.39 %
  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:  1.10 (0.26), residues: 1086
  helix:  1.53 (0.21), residues: 618
  sheet: -1.13 (0.52), residues: 90
  loop :  0.02 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 414 
 TYR   0.015   0.001   TYR A 361 
 PHE   0.015   0.001   PHE B  44 
 TRP   0.005   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8792)
  covalent geometry    : angle       0.51694 (11868)
  hydrogen bonds       : bond        0.04229 (  483)
  hydrogen bonds       : angle       3.96427 ( 1407)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.5899 (mmtm) cc_final: 0.5689 (mmtm)
REVERT: A  198 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6421 (tt)
REVERT: A  321 MET cc_start: 0.6732 (ttp) cc_final: 0.6503 (mtp)
REVERT: B  357 GLU cc_start: 0.6325 (mm-30) cc_final: 0.5815 (mt-10)
REVERT: B  619 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.7170 (ttm-80)
  outliers start: 24
  outliers final: 17
  residues processed: 116
  average time/residue: 0.1139
  time to fit residues: 17.7666
Evaluate side-chains
  109 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 73 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0670
   chunk 35 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.9722

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
B 204 HIS
** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.217226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.190618 restraints weight = 8618.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.193897 restraints weight = 6466.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.196295 restraints weight = 5281.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.197851 restraints weight = 4545.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.198263 restraints weight = 4077.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8793  Z= 0.129
  Angle     :  0.543  14.960  11868  Z= 0.275
  Chirality :  0.040   0.138   1344
  Planarity :  0.004   0.047   1506
  Dihedral  :  9.505 179.115   1266
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.33 %
    Favored  : 81.85 %
  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:  1.09 (0.26), residues: 1086
  helix:  1.51 (0.21), residues: 618
  sheet: -1.15 (0.52), residues: 90
  loop :  0.03 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 414 
 TYR   0.017   0.001   TYR A 361 
 PHE   0.015   0.001   PHE B  44 
 TRP   0.003   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8792)
  covalent geometry    : angle       0.54255 (11868)
  hydrogen bonds       : bond        0.04466 (  483)
  hydrogen bonds       : angle       3.95961 ( 1407)
  Misc. bond           : bond        0.00023 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6421 (tt)
REVERT: A  522 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7055 (t)
REVERT: B  302 SER cc_start: 0.8061 (t) cc_final: 0.7744 (p)
REVERT: B  357 GLU cc_start: 0.6346 (mm-30) cc_final: 0.5943 (tt0)
REVERT: B  619 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7157 (ttm-80)
  outliers start: 26
  outliers final: 19
  residues processed: 114
  average time/residue: 0.1186
  time to fit residues: 18.2083
Evaluate side-chains
  113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    0.0060
   chunk 40 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0040
   chunk 66 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.7410

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
A 585 GLN
B 204 HIS
** B 585 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 = 0.4588 r_free = 0.4588 target = 0.227212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.200931 restraints weight = 8486.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.204526 restraints weight = 6264.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.207002 restraints weight = 5046.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.208129 restraints weight = 4311.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.209562 restraints weight = 3919.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8793  Z= 0.117
  Angle     :  0.528  13.165  11868  Z= 0.268
  Chirality :  0.039   0.153   1344
  Planarity :  0.004   0.047   1506
  Dihedral  :  9.332 179.298   1266
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.09 %
    Favored  : 81.41 %
  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:  1.24 (0.26), residues: 1086
  helix:  1.63 (0.21), residues: 618
  sheet: -1.07 (0.53), residues: 90
  loop :  0.10 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 317 
 TYR   0.016   0.001   TYR A 361 
 PHE   0.014   0.001   PHE B  44 
 TRP   0.004   0.001   TRP A 391 
 HIS   0.007   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8792)
  covalent geometry    : angle       0.52783 (11868)
  hydrogen bonds       : bond        0.04212 (  483)
  hydrogen bonds       : angle       3.87106 ( 1407)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6140 (tt)
REVERT: A  522 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.6962 (t)
REVERT: B  142 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6573 (mp)
REVERT: B  302 SER cc_start: 0.8010 (t) cc_final: 0.7705 (p)
REVERT: B  357 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5901 (tt0)
REVERT: B  619 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7170 (ttm-80)
  outliers start: 23
  outliers final: 19
  residues processed: 114
  average time/residue: 0.1209
  time to fit residues: 18.3830
Evaluate side-chains
  114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
B 204 HIS
** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.218069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.192947 restraints weight = 8478.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.194273 restraints weight = 7815.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.196457 restraints weight = 6717.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.197185 restraints weight = 5661.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.197818 restraints weight = 4866.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8793  Z= 0.125
  Angle     :  0.542  12.302  11868  Z= 0.274
  Chirality :  0.040   0.188   1344
  Planarity :  0.004   0.045   1506
  Dihedral  :  9.271 178.453   1266
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.85 %
    Favored  : 80.33 %
  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:  1.20 (0.26), residues: 1086
  helix:  1.60 (0.21), residues: 620
  sheet: -1.12 (0.53), residues: 90
  loop :  0.07 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 518 
 TYR   0.016   0.001   TYR A 361 
 PHE   0.010   0.001   PHE B  44 
 TRP   0.003   0.001   TRP B 391 
 HIS   0.007   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8792)
  covalent geometry    : angle       0.54218 (11868)
  hydrogen bonds       : bond        0.04319 (  483)
  hydrogen bonds       : angle       3.88122 ( 1407)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6091 (tt)
REVERT: A  321 MET cc_start: 0.6814 (ttm) cc_final: 0.6535 (mtp)
REVERT: A  522 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7010 (t)
REVERT: B  142 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6679 (mp)
REVERT: B  302 SER cc_start: 0.8050 (t) cc_final: 0.7700 (p)
REVERT: B  357 GLU cc_start: 0.6353 (mm-30) cc_final: 0.5924 (tt0)
REVERT: B  367 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5675 (mp)
REVERT: B  619 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.7148 (ttm-80)
  outliers start: 26
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1014
  time to fit residues: 15.1610
Evaluate side-chains
  114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  516 LEU
Chi-restraints excluded: chain B residue  544 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 85 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0270
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
B 204 HIS
** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.219436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.192252 restraints weight = 8548.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.195646 restraints weight = 6385.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.198130 restraints weight = 5180.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.199672 restraints weight = 4471.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.201016 restraints weight = 4021.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.4358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8793  Z= 0.115
  Angle     :  0.534  11.664  11868  Z= 0.269
  Chirality :  0.039   0.172   1344
  Planarity :  0.004   0.045   1506
  Dihedral  :  9.138 177.930   1266
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 17.39 %
    Favored  : 80.54 %
  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:  1.36 (0.26), residues: 1086
  helix:  1.76 (0.21), residues: 610
  sheet: -1.00 (0.54), residues: 90
  loop :  0.10 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 518 
 TYR   0.015   0.001   TYR A 361 
 PHE   0.008   0.001   PHE A 178 
 TRP   0.004   0.001   TRP A 391 
 HIS   0.007   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8792)
  covalent geometry    : angle       0.53446 (11868)
  hydrogen bonds       : bond        0.04085 (  483)
  hydrogen bonds       : angle       3.81961 ( 1407)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6091 (tt)
REVERT: A  522 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.6918 (t)
REVERT: B  142 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6569 (mp)
REVERT: B  302 SER cc_start: 0.8014 (t) cc_final: 0.7676 (p)
REVERT: B  357 GLU cc_start: 0.6297 (mm-30) cc_final: 0.5903 (tt0)
REVERT: B  367 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5704 (mp)
REVERT: B  619 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7129 (ttm-80)
  outliers start: 19
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0977
  time to fit residues: 15.0136
Evaluate side-chains
  113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  429 ASN
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  142 LEU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0670
   chunk 79 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
B 204 HIS
** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.219123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.191644 restraints weight = 8586.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.195078 restraints weight = 6466.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.197499 restraints weight = 5261.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.199215 restraints weight = 4548.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.200240 restraints weight = 4091.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6764
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8793  Z= 0.115
  Angle     :  0.540  12.705  11868  Z= 0.269
  Chirality :  0.039   0.170   1344
  Planarity :  0.004   0.044   1506
  Dihedral  :  9.026 177.042   1266
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.61 %
    Favored  : 79.78 %
  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:  1.38 (0.26), residues: 1086
  helix:  1.77 (0.21), residues: 610
  sheet: -0.93 (0.55), residues: 90
  loop :  0.10 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 414 
 TYR   0.015   0.001   TYR A 361 
 PHE   0.009   0.001   PHE A 178 
 TRP   0.003   0.001   TRP B 391 
 HIS   0.007   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8792)
  covalent geometry    : angle       0.53976 (11868)
  hydrogen bonds       : bond        0.04090 (  483)
  hydrogen bonds       : angle       3.80669 ( 1407)
  Misc. bond           : bond        0.00021 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1304.05 seconds
wall clock time: 23 minutes 36.08 seconds (1416.08 seconds total)