Starting phenix.real_space_refine
on Thu Mar 13 09:09:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8phf_17660/03_2025/8phf_17660.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8phf_17660/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8phf_17660/03_2025/8phf_17660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8phf_17660/03_2025/8phf_17660.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8phf_17660/03_2025/8phf_17660.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8phf_17660/03_2025/8phf_17660.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.56, per 1000 atoms: 0.64
  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: 2.23
  Conformation dependent library (CDL) restraints added in 987.5 milliseconds
  

  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: 0.88
  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: 2.30

  Time building geometry restraints manager: 2.62 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: 0.04
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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     22.500
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.310
-------------------------------------------------------------------------------
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   8792  Z= 0.286
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (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
 TRP   0.004   0.001   TRP B 213 
 HIS   0.007   0.001   HIS A 204 
 PHE   0.031   0.002   PHE A 425 
 TYR   0.021   0.001   TYR B 361 
 ARG   0.006   0.000   ARG A 609 

*********************** 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  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.7705 (m-30) cc_final: 0.7184 (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: 0.2453
  time to fit residues: 41.0946
Evaluate side-chains
  94 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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 91 optimal weight:    0.0050
   chunk 81 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0970
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.4792

-------------------------------------------------------------------------------
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 161 GLN
B 204 HIS
B 527 GLN
B 585 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.224056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.200430 restraints weight = 8290.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.203593 restraints weight = 7648.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.204866 restraints weight = 5625.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8792  Z= 0.162
  Angle     :  0.552   8.741  11868  Z= 0.283
  Chirality :  0.039   0.146   1344
  Planarity :  0.004   0.045   1506
  Dihedral  : 11.010 166.987   1267
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  7.07 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 1086
  helix:  1.69 (0.21), residues: 610
  sheet: -1.02 (0.51), residues: 90
  loop :  0.22 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 213 
 HIS   0.008   0.001   HIS B 204 
 PHE   0.013   0.001   PHE B 275 
 TYR   0.019   0.001   TYR B 435 
 ARG   0.002   0.000   ARG B 414 

*********************** 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
  125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
REVERT: B  357 GLU cc_start: 0.6392 (mm-30) cc_final: 0.5857 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 119
  average time/residue: 0.3092
  time to fit residues: 49.3687
Evaluate side-chains
  102 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  327 CYS
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0980
   chunk 82 optimal weight:    3.9990
   chunk 105 optimal weight:    0.0270
   chunk 68 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5038

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 HIS
B 331 GLN
** 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 = 0.4636 r_free = 0.4636 target = 0.233853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.208328 restraints weight = 8386.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.211996 restraints weight = 6118.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.214362 restraints weight = 4870.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8792  Z= 0.145
  Angle     :  0.501   7.401  11868  Z= 0.258
  Chirality :  0.038   0.135   1344
  Planarity :  0.004   0.044   1506
  Dihedral  :  9.666 170.632   1267
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.11 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.26), residues: 1086
  helix:  1.80 (0.21), residues: 610
  sheet: -0.88 (0.52), residues: 90
  loop :  0.28 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 391 
 HIS   0.002   0.001   HIS B 491 
 PHE   0.009   0.001   PHE A 178 
 TYR   0.018   0.001   TYR A 361 
 ARG   0.003   0.000   ARG B 518 

*********************** 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
  126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
  outliers start: 20
  outliers final: 13
  residues processed: 118
  average time/residue: 0.2419
  time to fit residues: 38.8708
Evaluate side-chains
  105 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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  360 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  558 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 87 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0570
   chunk 20 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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 216 ASN
B 585 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.222157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.195155 restraints weight = 8477.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.198805 restraints weight = 6232.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.201245 restraints weight = 5015.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8792  Z= 0.158
  Angle     :  0.490   6.086  11868  Z= 0.253
  Chirality :  0.038   0.137   1344
  Planarity :  0.003   0.043   1506
  Dihedral  :  9.547 174.766   1266
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.72 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.26), residues: 1086
  helix:  1.78 (0.21), residues: 614
  sheet: -0.83 (0.52), residues: 90
  loop :  0.18 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 213 
 HIS   0.006   0.001   HIS B 204 
 PHE   0.022   0.001   PHE B 508 
 TYR   0.017   0.001   TYR A 361 
 ARG   0.002   0.000   ARG B 317 

*********************** 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
  123 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 15
  residues processed: 116
  average time/residue: 0.2428
  time to fit residues: 38.0373
Evaluate side-chains
  104 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  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 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  356 MET
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 38 optimal weight:    0.0050
   chunk 85 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0040
   chunk 23 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 107 optimal weight:    0.3980
   overall best weight:    0.6208

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.222778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.195253 restraints weight = 8431.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.196222 restraints weight = 6963.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.200452 restraints weight = 5806.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8792  Z= 0.149
  Angle     :  0.477   5.837  11868  Z= 0.249
  Chirality :  0.038   0.143   1344
  Planarity :  0.003   0.040   1506
  Dihedral  :  9.482 177.704   1266
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.80 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.26), residues: 1086
  helix:  1.83 (0.21), residues: 614
  sheet: -0.83 (0.52), residues: 90
  loop :  0.22 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 491 
 PHE   0.015   0.001   PHE B 508 
 TYR   0.017   0.001   TYR A 361 
 ARG   0.002   0.000   ARG B 518 

*********************** 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
  122 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.946 
Fit side-chains
REVERT: B  276 GLU cc_start: 0.6114 (pp20) cc_final: 0.5862 (pp20)
  outliers start: 19
  outliers final: 16
  residues processed: 114
  average time/residue: 0.2584
  time to fit residues: 39.0007
Evaluate side-chains
  110 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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  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 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  356 MET
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 67 optimal weight:    0.0970
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 78 optimal weight:    0.4980
   chunk 92 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.4382

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
B 331 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.216351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.189030 restraints weight = 8417.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.192469 restraints weight = 6328.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.194688 restraints weight = 5165.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8792  Z= 0.232
  Angle     :  0.556   7.072  11868  Z= 0.287
  Chirality :  0.040   0.137   1344
  Planarity :  0.004   0.041   1506
  Dihedral  :  9.483 178.860   1266
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 14.35 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1086
  helix:  1.52 (0.21), residues: 618
  sheet: -1.10 (0.52), residues: 90
  loop :  0.12 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 213 
 HIS   0.005   0.001   HIS B 563 
 PHE   0.017   0.002   PHE B  44 
 TYR   0.018   0.001   TYR A 361 
 ARG   0.003   0.000   ARG B 304 

*********************** 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
  126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.968 
Fit side-chains
REVERT: B  304 ARG cc_start: 0.6865 (ptp90) cc_final: 0.6360 (mtm110)
  outliers start: 29
  outliers final: 23
  residues processed: 113
  average time/residue: 0.2699
  time to fit residues: 40.4519
Evaluate side-chains
  114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
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  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 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  327 CYS
Chi-restraints excluded: chain B residue  356 MET
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
B 204 HIS
** B 216 ASN ** 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 = 0.4448 r_free = 0.4448 target = 0.211501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.184546 restraints weight = 8655.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.187382 restraints weight = 8589.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.188355 restraints weight = 6554.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8792  Z= 0.267
  Angle     :  0.598   7.268  11868  Z= 0.307
  Chirality :  0.042   0.145   1344
  Planarity :  0.004   0.041   1506
  Dihedral  :  9.485 178.545   1266
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.89 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.26), residues: 1086
  helix:  1.21 (0.21), residues: 618
  sheet: -1.27 (0.51), residues: 90
  loop : -0.02 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 213 
 HIS   0.006   0.001   HIS B 563 
 PHE   0.021   0.002   PHE B  44 
 TYR   0.018   0.001   TYR A 361 
 ARG   0.006   0.000   ARG B 329 

*********************** 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
  125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.935 
Fit side-chains
REVERT: B  302 SER cc_start: 0.8192 (t) cc_final: 0.7907 (p)
REVERT: B  341 LEU cc_start: 0.7644 (mt) cc_final: 0.7406 (mt)
  outliers start: 26
  outliers final: 21
  residues processed: 113
  average time/residue: 0.2721
  time to fit residues: 40.6973
Evaluate side-chains
  111 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
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  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  327 CYS
Chi-restraints excluded: chain B residue  356 MET
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 71 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 41 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 216 ASN
B 504 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.217895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.190713 restraints weight = 8644.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.194312 restraints weight = 6376.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.196369 restraints weight = 5146.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8792  Z= 0.178
  Angle     :  0.536   8.166  11868  Z= 0.276
  Chirality :  0.040   0.134   1344
  Planarity :  0.004   0.042   1506
  Dihedral  :  9.264 178.929   1266
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.54 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1086
  helix:  1.50 (0.21), residues: 620
  sheet: -1.15 (0.52), residues: 90
  loop :  0.04 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 391 
 HIS   0.004   0.001   HIS B 204 
 PHE   0.016   0.001   PHE B  44 
 TYR   0.017   0.001   TYR A 361 
 ARG   0.002   0.000   ARG B 329 

*********************** 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: 25
    poor density    : 97
  time to evaluate  : 0.955 
Fit side-chains
REVERT: B  283 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6757 (pt0)
REVERT: B  302 SER cc_start: 0.8094 (t) cc_final: 0.7768 (p)
  outliers start: 25
  outliers final: 21
  residues processed: 113
  average time/residue: 0.2928
  time to fit residues: 45.4280
Evaluate side-chains
  113 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  544 THR
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  283 GLU
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  356 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 106 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0010
   chunk 107 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9188

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.217371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.190391 restraints weight = 8582.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.193620 restraints weight = 6402.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.195828 restraints weight = 5197.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6838
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8792  Z= 0.188
  Angle     :  0.542   7.336  11868  Z= 0.278
  Chirality :  0.040   0.176   1344
  Planarity :  0.004   0.043   1506
  Dihedral  :  9.226 178.261   1266
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.87 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 1086
  helix:  1.53 (0.21), residues: 618
  sheet: -1.15 (0.53), residues: 90
  loop :  0.05 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 391 
 HIS   0.004   0.001   HIS B 204 
 PHE   0.011   0.001   PHE B 508 
 TYR   0.017   0.001   TYR A 361 
 ARG   0.001   0.000   ARG A 266 

*********************** 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
  119 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 1.790 
Fit side-chains
REVERT: B  302 SER cc_start: 0.8108 (t) cc_final: 0.7770 (p)
  outliers start: 23
  outliers final: 22
  residues processed: 108
  average time/residue: 0.3182
  time to fit residues: 47.4975
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  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  544 THR
Chi-restraints excluded: chain A residue  554 ILE
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  215 THR
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  356 MET
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 41 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 85 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0670
   chunk 95 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0370
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.3596

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.223030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.196114 restraints weight = 8466.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.199724 restraints weight = 6235.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.202282 restraints weight = 5027.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.4363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8792  Z= 0.143
  Angle     :  0.511   6.488  11868  Z= 0.263
  Chirality :  0.039   0.174   1344
  Planarity :  0.003   0.043   1506
  Dihedral  :  9.115 178.752   1266
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.07 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1086
  helix:  1.77 (0.21), residues: 620
  sheet: -1.01 (0.53), residues: 90
  loop :  0.08 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 391 
 HIS   0.004   0.001   HIS B 204 
 PHE   0.011   0.001   PHE B 508 
 TYR   0.014   0.001   TYR A 361 
 ARG   0.002   0.000   ARG A 414 

********************** 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
  109 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.958 
Fit side-chains
  outliers start: 15
  outliers final: 13
  residues processed: 104
  average time/residue: 0.2647
  time to fit residues: 36.4773
Evaluate side-chains
  101 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  309 SER
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  585 GLN
Chi-restraints excluded: chain B residue  215 THR
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  356 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0470
   chunk 94 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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 216 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.220414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.192659 restraints weight = 8548.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.196279 restraints weight = 6403.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.198364 restraints weight = 5205.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8792  Z= 0.168
  Angle     :  0.520   6.488  11868  Z= 0.267
  Chirality :  0.039   0.158   1344
  Planarity :  0.004   0.044   1506
  Dihedral  :  9.117 178.305   1266
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.39 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.26), residues: 1086
  helix:  1.76 (0.21), residues: 620
  sheet: -1.03 (0.53), residues: 90
  loop :  0.08 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 391 
 HIS   0.004   0.001   HIS B 204 
 PHE   0.010   0.001   PHE B 508 
 TYR   0.016   0.001   TYR A 361 
 ARG   0.003   0.000   ARG B 532 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2548.10 seconds
wall clock time: 46 minutes 38.49 seconds (2798.49 seconds total)