Starting phenix.real_space_refine
on Sat May 10 09:10:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fk5_50519/05_2025/9fk5_50519.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fk5_50519/05_2025/9fk5_50519.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fk5_50519/05_2025/9fk5_50519.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fk5_50519/05_2025/9fk5_50519.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fk5_50519/05_2025/9fk5_50519.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fk5_50519/05_2025/9fk5_50519.cif"
  }
  resolution = 4.1
  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=  -0.000 sd=   0.016
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: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    3636      2.51       5
     N     981      2.21       5
     O    1093      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5765
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 890
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102}
    Chain: "B"
      Number of atoms: 879
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 879
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 586
          Classifications: {'peptide': 77}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 831
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 6, 'TRANS': 98}
    Chain: "E"
      Number of atoms: 2579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2579
          Classifications: {'peptide': 329}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 309}
  Time building chain proxies: 5.29, per 1000 atoms: 0.92
  Number of scatterers: 5765
  At special positions: 0
  Unit cell: (81.34, 74.7, 138.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1093      8.00
     N     981      7.00
     C    3636      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=22, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 307 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 315 " - pdb=" SG  CYS A 378 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 409 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 348 " - pdb=" SG  CYS A 411 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 377 " - pdb=" SG  CYS B 377 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 307 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 315 " - pdb=" SG  CYS B 378 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 344 " - pdb=" SG  CYS B 409 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 348 " - pdb=" SG  CYS B 411 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  34 " - pdb=" SG  CYS C  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C  98 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  99 " - pdb=" SG  CYS C 104 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  51 " - pdb=" SG  CYS D  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  77 " - pdb=" SG  CYS D 101 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 121 " - pdb=" SG  CYS D 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 138 " - pdb=" SG  CYS D 143 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  31 " - pdb=" SG  CYS E 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  55 " - pdb=" SG  CYS E 201 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.53
  Conformation dependent library (CDL) restraints added in 748.2 milliseconds
  

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 18 sheets defined
      13.7% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 303 through 310
    Processing helix  chain 'A' and resid 356 through 369
    Processing helix  chain 'A' and resid 370 through 373
      removed outlier: 3.655A  pdb=" N   SER A 373 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 370 through 373'
    Processing helix  chain 'B' and resid 303 through 310
      removed outlier: 3.732A  pdb=" N   ARG B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 329
    Processing helix  chain 'B' and resid 356 through 369
    Processing helix  chain 'D' and resid 142 through 144
      No H-bonds generated for 'chain 'D' and resid 142 through 144'
    Processing helix  chain 'E' and resid 58 through 62
      removed outlier: 3.793A  pdb=" N   SER E  62 " --> pdb=" O   GLY E  59 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 149
      removed outlier: 3.797A  pdb=" N   PHE E 146 " --> pdb=" O   VAL E 143 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LYS E 148 " --> pdb=" O   ASN E 145 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 173
    Processing helix  chain 'E' and resid 305 through 311
      removed outlier: 3.519A  pdb=" N   LEU E 311 " --> pdb=" O   ASP E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 325 through 335
    Processing sheet with id=AA1, first strand: chain 'A' and resid 316 through 318
      removed outlier: 3.811A  pdb=" N   PHE A 343 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323
    Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 380
    Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 392
      removed outlier: 5.717A  pdb=" N   GLU A 384 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASN A 403 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 316 through 318
      removed outlier: 3.530A  pdb=" N   SER B 345 " --> pdb=" O   CYS B 316 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 323
    Processing sheet with id=AA7, first strand: chain 'B' and resid 333 through 335
      removed outlier: 6.570A  pdb=" N   VAL B 333 " --> pdb=" O   TYR B 391 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   TYR B 391 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU B 335 " --> pdb=" O   LEU B 389 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   SER B 408 " --> pdb=" O   GLN B 381 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU B 383 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL B 406 " --> pdb=" O   LEU B 383 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   MET B 404 " --> pdb=" O   PRO B 385 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   THR B 387 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 8.823A  pdb=" N   SER B 402 " --> pdb=" O   THR B 387 " (cutoff:3.500A)
      removed outlier: 9.724A  pdb=" N   LEU B 389 " --> pdb=" O   GLN B 400 " (cutoff:3.500A)
      removed outlier: 10.129A  pdb=" N   GLN B 400 " --> pdb=" O   LEU B 389 " (cutoff:3.500A)
      removed outlier: 9.700A  pdb=" N   TYR B 391 " --> pdb=" O   VAL B 398 " (cutoff:3.500A)
      removed outlier: 9.430A  pdb=" N   VAL B 398 " --> pdb=" O   TYR B 391 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 34
    Processing sheet with id=AA9, first strand: chain 'C' and resid 63 through 70
      removed outlier: 4.148A  pdb=" N   VAL C  93 " --> pdb=" O   GLU C  58 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 52
    Processing sheet with id=AB2, first strand: chain 'D' and resid 57 through 58
      removed outlier: 4.138A  pdb=" N   THR D 132 " --> pdb=" O   LYS D  90 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   MET D 135 " --> pdb=" O   LYS D 124 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 66 through 68
      removed outlier: 6.728A  pdb=" N   CYS D 121 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 34 through 35
      removed outlier: 3.653A  pdb=" N   LEU E  34 " --> pdb=" O   GLY E 224 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 215 through 220
      removed outlier: 4.427A  pdb=" N   ALA E  44 " --> pdb=" O   GLN E 220 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   PHE E 353 " --> pdb=" O   ASP E 253 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   ILE E 255 " --> pdb=" O   PHE E 353 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   LEU E 355 " --> pdb=" O   ILE E 255 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ASP E 257 " --> pdb=" O   LEU E 355 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   LEU E 357 " --> pdb=" O   ASP E 257 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ARG E 259 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   SER E 303 " --> pdb=" O   VAL E 281 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   TRP E 283 " --> pdb=" O   SER E 303 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 56
      removed outlier: 5.673A  pdb=" N   VAL E  67 " --> pdb=" O   SER E 177 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   SER E 179 " --> pdb=" O   VAL E  67 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   ILE E  69 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE E 130 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 91
      removed outlier: 5.962A  pdb=" N   HIS E  90 " --> pdb=" O   ILE E 189 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 312 through 314
      removed outlier: 7.268A  pdb=" N   GLY E 292 " --> pdb=" O   GLN E 313 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   ARG E 269 " --> pdb=" O   LYS E 293 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   GLU E 295 " --> pdb=" O   ARG E 269 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL E 271 " --> pdb=" O   GLU E 295 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   MET E 297 " --> pdb=" O   VAL E 271 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   LEU E 273 " --> pdb=" O   MET E 297 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   TYR E 344 " --> pdb=" O   HIS E 237 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE E 239 " --> pdb=" O   TYR E 344 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASN E 346 " --> pdb=" O   ILE E 239 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LEU E 241 " --> pdb=" O   ASN E 346 " (cutoff:3.500A)

    162 hydrogen bonds defined for protein.
    429 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: 1.73

  Time building geometry restraints manager: 1.80 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1117
        1.33 -     1.45: 1398
        1.45 -     1.57: 3320
        1.57 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 5901
  Sorted by residual:
  bond pdb=" C   SER D 118 "
       pdb=" O   SER D 118 "
    ideal  model  delta    sigma   weight residual
    1.235  1.203  0.032 1.28e-02 6.10e+03 6.26e+00
  bond pdb=" N   SER D 118 "
       pdb=" CA  SER D 118 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.37e-02 5.33e+03 6.12e+00
  bond pdb=" N   THR E 317 "
       pdb=" CA  THR E 317 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.23e-02 6.61e+03 5.51e+00
  bond pdb=" C   PRO D 119 "
       pdb=" O   PRO D 119 "
    ideal  model  delta    sigma   weight residual
    1.235  1.205  0.030 1.30e-02 5.92e+03 5.25e+00
  bond pdb=" N   ASN E  71 "
       pdb=" CA  ASN E  71 "
    ideal  model  delta    sigma   weight residual
    1.463  1.487 -0.025 1.28e-02 6.10e+03 3.70e+00
  ... (remaining 5896 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.84: 7418
        0.84 -     1.69: 464
        1.69 -     2.53: 83
        2.53 -     3.37: 41
        3.37 -     4.22: 16
  Bond angle restraints: 8022
  Sorted by residual:
  angle pdb=" CA  SER D 118 "
        pdb=" C   SER D 118 "
        pdb=" O   SER D 118 "
      ideal   model   delta    sigma   weight residual
     120.69  117.06    3.63 1.13e+00 7.83e-01 1.03e+01
  angle pdb=" N   GLY E 292 "
        pdb=" CA  GLY E 292 "
        pdb=" C   GLY E 292 "
      ideal   model   delta    sigma   weight residual
     111.21  114.49   -3.28 1.04e+00 9.25e-01 9.92e+00
  angle pdb=" CA  ASN E  71 "
        pdb=" C   ASN E  71 "
        pdb=" O   ASN E  71 "
      ideal   model   delta    sigma   weight residual
     121.58  118.19    3.39 1.12e+00 7.97e-01 9.17e+00
  angle pdb=" CA  SER D 118 "
        pdb=" C   SER D 118 "
        pdb=" N   PRO D 119 "
      ideal   model   delta    sigma   weight residual
     117.79  121.00   -3.21 1.08e+00 8.57e-01 8.83e+00
  angle pdb=" CA  SER D 139 "
        pdb=" C   SER D 139 "
        pdb=" O   SER D 139 "
      ideal   model   delta    sigma   weight residual
     121.78  118.58    3.20 1.12e+00 7.97e-01 8.17e+00
  ... (remaining 8017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.50: 3326
       11.50 -    23.00: 236
       23.00 -    34.50: 59
       34.50 -    45.99: 19
       45.99 -    57.49: 8
  Dihedral angle restraints: 3648
    sinusoidal: 1490
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" CA  PHE E 141 "
           pdb=" C   PHE E 141 "
           pdb=" N   GLU E 142 "
           pdb=" CA  GLU E 142 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.80   19.20     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" N   CYS B 316 "
           pdb=" CA  CYS B 316 "
           pdb=" CB  CYS B 316 "
           pdb=" SG  CYS B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.49   57.49     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" N   CYS A 316 "
           pdb=" CA  CYS A 316 "
           pdb=" CB  CYS A 316 "
           pdb=" SG  CYS A 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.14  -56.86     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 3645 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 548
       0.030 -    0.061: 243
       0.061 -    0.091: 38
       0.091 -    0.121: 68
       0.121 -    0.151: 12
  Chirality restraints: 909
  Sorted by residual:
  chirality pdb=" CA  ILE D  76 "
            pdb=" N   ILE D  76 "
            pdb=" C   ILE D  76 "
            pdb=" CB  ILE D  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CA  VAL B 379 "
            pdb=" N   VAL B 379 "
            pdb=" C   VAL B 379 "
            pdb=" CB  VAL B 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  ILE E 187 "
            pdb=" N   ILE E 187 "
            pdb=" C   ILE E 187 "
            pdb=" CB  ILE E 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 906 not shown)

  Planarity restraints: 1036
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 379 "    0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO B 380 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 380 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 380 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  92 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO E  93 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO E  93 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E  93 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D  47 "    0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO D  48 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO D  48 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D  48 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1033 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 85
        2.60 -     3.18: 4998
        3.18 -     3.75: 8358
        3.75 -     4.33: 12057
        4.33 -     4.90: 19917
  Nonbonded interactions: 45415
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 399 "
            pdb=" OG  SER E 246 "
     model   vdw
     2.030 3.040
  nonbonded pdb=" O   GLY E 144 "
            pdb=" OG  SER E 147 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" O   ALA A 372 "
            pdb=" OG  SER A 373 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OG1 THR C  59 "
            pdb=" O   LYS C  62 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" OG  SER E 222 "
            pdb=" OG1 THR E 347 "
     model   vdw
     2.134 3.040
  ... (remaining 45410 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 301 through 324 or resid 326 through 389 or resid 391 thro \ 
ugh 393 or resid 395 through 412))
  selection = (chain 'B' and (resid 301 through 324 or resid 326 through 389 or resid 391 thro \ 
ugh 393 or resid 395 through 412))
}

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:             3.100
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.270
  Find NCS groups from input model:        0.110
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6080
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      :  0.003   0.034   5923  Z= 0.159
  Angle     :  0.523   4.218   8066  Z= 0.297
  Chirality :  0.044   0.151    909
  Planarity :  0.004   0.042   1036
  Dihedral  :  9.259  57.492   2176
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  4.20 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.88 (0.32), residues: 725
  helix:  0.47 (0.59), residues: 86
  sheet: -0.46 (0.32), residues: 268
  loop : -0.85 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  88 
 HIS   0.003   0.001   HIS C  37 
 PHE   0.012   0.001   PHE E  49 
 TYR   0.012   0.001   TYR A 365 
 ARG   0.003   0.000   ARG A 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26920 (  162)
  hydrogen bonds       : angle      11.49290 (  429)
  SS BOND              : bond        0.00467 (   22)
  SS BOND              : angle       1.15289 (   44)
  covalent geometry    : bond        0.00300 ( 5901)
  covalent geometry    : angle       0.51791 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8349 (mt) cc_final: 0.7619 (tp)
REVERT: B  404 MET cc_start: 0.8193 (mmm) cc_final: 0.7369 (mmm)
  outliers start: 15
  outliers final: 8
  residues processed: 169
  average time/residue: 0.2076
  time to fit residues: 44.1117
Evaluate side-chains
  91 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.086918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.072622 restraints weight = 21076.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.074566 restraints weight = 12851.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.076033 restraints weight = 9082.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6473
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5923  Z= 0.155
  Angle     :  0.603   6.081   8066  Z= 0.318
  Chirality :  0.047   0.182    909
  Planarity :  0.005   0.037   1036
  Dihedral  :  4.493  17.915    779
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.90 (0.31), residues: 725
  helix:  0.75 (0.59), residues: 83
  sheet: -0.63 (0.32), residues: 262
  loop : -0.79 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  88 
 HIS   0.004   0.001   HIS B 334 
 PHE   0.013   0.001   PHE B 308 
 TYR   0.013   0.002   TYR B 339 
 ARG   0.006   0.001   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04407 (  162)
  hydrogen bonds       : angle       7.95024 (  429)
  SS BOND              : bond        0.00381 (   22)
  SS BOND              : angle       1.77776 (   44)
  covalent geometry    : bond        0.00355 ( 5901)
  covalent geometry    : angle       0.59018 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8215 (mt) cc_final: 0.7512 (mt)
REVERT: B  399 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6766 (mt-10)
REVERT: E  257 ASP cc_start: 0.8561 (m-30) cc_final: 0.8277 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1937
  time to fit residues: 25.8985
Evaluate side-chains
  67 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 334 HIS
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 237 HIS
E 352 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.092907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.080013 restraints weight = 19624.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.080909 restraints weight = 13792.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.081968 restraints weight = 11986.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6466
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5923  Z= 0.125
  Angle     :  0.545   5.703   8066  Z= 0.286
  Chirality :  0.046   0.178    909
  Planarity :  0.004   0.038   1036
  Dihedral  :  4.338  18.081    779
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.73 (0.31), residues: 725
  helix:  0.87 (0.60), residues: 82
  sheet: -0.31 (0.35), residues: 228
  loop : -0.84 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.009   0.001   PHE D 133 
 TYR   0.012   0.001   TYR E 216 
 ARG   0.003   0.000   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  162)
  hydrogen bonds       : angle       7.12169 (  429)
  SS BOND              : bond        0.00327 (   22)
  SS BOND              : angle       1.17788 (   44)
  covalent geometry    : bond        0.00275 ( 5901)
  covalent geometry    : angle       0.53913 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8190 (mt) cc_final: 0.7525 (mt)
REVERT: D  123 MET cc_start: 0.7523 (mmm) cc_final: 0.7052 (mmm)
REVERT: D  124 LYS cc_start: 0.8418 (mmpt) cc_final: 0.8170 (mmmt)
REVERT: E  257 ASP cc_start: 0.8550 (m-30) cc_final: 0.8306 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1684
  time to fit residues: 20.8678
Evaluate side-chains
  66 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   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 366 ASN
B 334 HIS
B 381 GLN
D  49 GLN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.092097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.078962 restraints weight = 20252.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.080546 restraints weight = 17594.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.082419 restraints weight = 13067.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5923  Z= 0.135
  Angle     :  0.537   5.640   8066  Z= 0.281
  Chirality :  0.045   0.169    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.366  17.368    779
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.31 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.31), residues: 725
  helix:  0.76 (0.61), residues: 82
  sheet: -0.35 (0.34), residues: 248
  loop : -0.85 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.008   0.001   PHE D 133 
 TYR   0.023   0.001   TYR A 306 
 ARG   0.004   0.000   ARG B 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  162)
  hydrogen bonds       : angle       6.89366 (  429)
  SS BOND              : bond        0.00388 (   22)
  SS BOND              : angle       1.37774 (   44)
  covalent geometry    : bond        0.00297 ( 5901)
  covalent geometry    : angle       0.52884 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8323 (mt) cc_final: 0.7663 (mt)
REVERT: D  123 MET cc_start: 0.7440 (mmm) cc_final: 0.6989 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1842
  time to fit residues: 21.4166
Evaluate side-chains
  62 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 57 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.090230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.076926 restraints weight = 20039.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.078210 restraints weight = 14498.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.079274 restraints weight = 12421.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5923  Z= 0.155
  Angle     :  0.569   6.734   8066  Z= 0.294
  Chirality :  0.046   0.168    909
  Planarity :  0.004   0.044   1036
  Dihedral  :  4.549  17.124    779
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.88 (0.31), residues: 725
  helix:  0.40 (0.59), residues: 87
  sheet: -0.51 (0.33), residues: 247
  loop : -0.79 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.010   0.001   HIS E  68 
 PHE   0.009   0.001   PHE C  44 
 TYR   0.018   0.002   TYR A 306 
 ARG   0.011   0.001   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03535 (  162)
  hydrogen bonds       : angle       6.72320 (  429)
  SS BOND              : bond        0.00413 (   22)
  SS BOND              : angle       1.66953 (   44)
  covalent geometry    : bond        0.00350 ( 5901)
  covalent geometry    : angle       0.55651 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8368 (mt) cc_final: 0.7673 (mt)
REVERT: A  404 MET cc_start: 0.7996 (tpp) cc_final: 0.7789 (tpp)
REVERT: D  123 MET cc_start: 0.7449 (mmm) cc_final: 0.7130 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1681
  time to fit residues: 18.8990
Evaluate side-chains
  59 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
B 366 ASN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  90 HIS
E 169 HIS
E 327 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.089403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.076440 restraints weight = 20127.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.077598 restraints weight = 14497.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.079040 restraints weight = 11793.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6617
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5923  Z= 0.174
  Angle     :  0.578   5.604   8066  Z= 0.300
  Chirality :  0.046   0.165    909
  Planarity :  0.004   0.036   1036
  Dihedral  :  4.736  18.180    779
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.02 (0.31), residues: 725
  helix:  0.06 (0.57), residues: 88
  sheet: -0.54 (0.33), residues: 238
  loop : -0.88 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  88 
 HIS   0.012   0.001   HIS E  68 
 PHE   0.010   0.001   PHE C  44 
 TYR   0.017   0.002   TYR A 306 
 ARG   0.005   0.001   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  162)
  hydrogen bonds       : angle       6.70904 (  429)
  SS BOND              : bond        0.00506 (   22)
  SS BOND              : angle       1.55040 (   44)
  covalent geometry    : bond        0.00392 ( 5901)
  covalent geometry    : angle       0.56855 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8355 (mt) cc_final: 0.7648 (mt)
REVERT: A  404 MET cc_start: 0.8089 (tpp) cc_final: 0.7476 (tpp)
REVERT: D  105 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7366 (pptt)
REVERT: D  123 MET cc_start: 0.7265 (mmm) cc_final: 0.6856 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1880
  time to fit residues: 20.2221
Evaluate side-chains
  61 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 169 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.090700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.077865 restraints weight = 20058.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.080475 restraints weight = 15251.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.080767 restraints weight = 10126.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5923  Z= 0.119
  Angle     :  0.556   6.861   8066  Z= 0.287
  Chirality :  0.045   0.166    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.639  19.455    779
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.59 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.92 (0.31), residues: 725
  helix:  0.68 (0.61), residues: 80
  sheet: -0.46 (0.34), residues: 238
  loop : -0.93 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.007   0.001   HIS E  68 
 PHE   0.008   0.001   PHE D 133 
 TYR   0.022   0.002   TYR B 339 
 ARG   0.005   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  162)
  hydrogen bonds       : angle       6.68034 (  429)
  SS BOND              : bond        0.00292 (   22)
  SS BOND              : angle       1.51102 (   44)
  covalent geometry    : bond        0.00270 ( 5901)
  covalent geometry    : angle       0.54601 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8411 (mt) cc_final: 0.7699 (mt)
REVERT: D  105 LYS cc_start: 0.7744 (mmtp) cc_final: 0.7329 (pptt)
REVERT: D  123 MET cc_start: 0.7243 (mmm) cc_final: 0.6835 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1646
  time to fit residues: 16.7528
Evaluate side-chains
  61 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    9.9990
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.091888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.078532 restraints weight = 19769.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.079780 restraints weight = 14908.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.080781 restraints weight = 13250.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6546
moved from start:          0.5083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5923  Z= 0.106
  Angle     :  0.542   7.962   8066  Z= 0.280
  Chirality :  0.045   0.164    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.401  17.343    779
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.59 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -0.89 (0.31), residues: 725
  helix:  0.38 (0.59), residues: 86
  sheet: -0.53 (0.33), residues: 244
  loop : -0.78 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.005   0.001   HIS E  68 
 PHE   0.009   0.001   PHE D 133 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.004   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03178 (  162)
  hydrogen bonds       : angle       6.37821 (  429)
  SS BOND              : bond        0.00283 (   22)
  SS BOND              : angle       1.77428 (   44)
  covalent geometry    : bond        0.00241 ( 5901)
  covalent geometry    : angle       0.52690 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8418 (mt) cc_final: 0.7691 (mt)
REVERT: D  105 LYS cc_start: 0.7732 (mmtp) cc_final: 0.7325 (pptt)
REVERT: D  123 MET cc_start: 0.7234 (mmm) cc_final: 0.6897 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2000
  time to fit residues: 22.6127
Evaluate side-chains
  60 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.091218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.077940 restraints weight = 20066.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.079163 restraints weight = 14605.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.080302 restraints weight = 12816.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5923  Z= 0.120
  Angle     :  0.548   7.934   8066  Z= 0.282
  Chirality :  0.045   0.158    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.406  17.230    779
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.72 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.03 (0.31), residues: 725
  helix:  0.05 (0.57), residues: 92
  sheet: -0.62 (0.33), residues: 244
  loop : -0.82 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  88 
 HIS   0.008   0.001   HIS E  68 
 PHE   0.009   0.001   PHE B 324 
 TYR   0.017   0.001   TYR A 306 
 ARG   0.004   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03153 (  162)
  hydrogen bonds       : angle       6.28046 (  429)
  SS BOND              : bond        0.00319 (   22)
  SS BOND              : angle       1.71962 (   44)
  covalent geometry    : bond        0.00273 ( 5901)
  covalent geometry    : angle       0.53405 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8374 (mt) cc_final: 0.7576 (tp)
REVERT: D  105 LYS cc_start: 0.7779 (mmtp) cc_final: 0.7410 (pptt)
REVERT: D  123 MET cc_start: 0.7333 (mmm) cc_final: 0.7029 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1573
  time to fit residues: 15.4469
Evaluate side-chains
  58 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.090656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.077650 restraints weight = 20201.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.079074 restraints weight = 14419.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.079922 restraints weight = 12416.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6580
moved from start:          0.5275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5923  Z= 0.121
  Angle     :  0.547   8.102   8066  Z= 0.282
  Chirality :  0.046   0.155    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.435  17.456    779
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.72 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.05 (0.31), residues: 725
  helix:  0.10 (0.57), residues: 92
  sheet: -0.69 (0.32), residues: 247
  loop : -0.81 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  88 
 HIS   0.008   0.001   HIS E  68 
 PHE   0.007   0.001   PHE D 133 
 TYR   0.017   0.001   TYR A 306 
 ARG   0.004   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03078 (  162)
  hydrogen bonds       : angle       6.23035 (  429)
  SS BOND              : bond        0.00324 (   22)
  SS BOND              : angle       1.66292 (   44)
  covalent geometry    : bond        0.00275 ( 5901)
  covalent geometry    : angle       0.53464 ( 8022)

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

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

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1450 Ramachandran restraints generated.
    725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8305 (mt) cc_final: 0.7689 (mt)
REVERT: D  105 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7451 (pptt)
REVERT: D  123 MET cc_start: 0.7327 (mmm) cc_final: 0.7047 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1570
  time to fit residues: 15.9569
Evaluate side-chains
  58 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 54 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.091025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.078287 restraints weight = 20152.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.079620 restraints weight = 14348.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.080817 restraints weight = 10664.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
moved from start:          0.5416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5923  Z= 0.111
  Angle     :  0.547   8.105   8066  Z= 0.281
  Chirality :  0.045   0.166    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.494  25.019    779
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.45 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    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: -1.03 (0.31), residues: 725
  helix:  0.12 (0.57), residues: 92
  sheet: -0.66 (0.33), residues: 242
  loop : -0.81 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.007   0.001   HIS E  68 
 PHE   0.007   0.001   PHE D 133 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.004   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02999 (  162)
  hydrogen bonds       : angle       6.16835 (  429)
  SS BOND              : bond        0.00295 (   22)
  SS BOND              : angle       1.59691 (   44)
  covalent geometry    : bond        0.00254 ( 5901)
  covalent geometry    : angle       0.53570 ( 8022)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2226.83 seconds
wall clock time: 39 minutes 50.43 seconds (2390.43 seconds total)