Starting phenix.real_space_refine
on Sun Apr 27 13:17:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fk5_50519/04_2025/9fk5_50519.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fk5_50519/04_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_50519/04_2025/9fk5_50519.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fk5_50519/04_2025/9fk5_50519.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fk5_50519/04_2025/9fk5_50519.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fk5_50519/04_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-5669/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: 5.06, per 1000 atoms: 0.88
  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: 1.34
  Conformation dependent library (CDL) restraints added in 682.6 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: 0.76
  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: 1.68

  Time building geometry restraints manager: 1.64 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:             4.270
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.710
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.520
-------------------------------------------------------------------------------
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  : 0.693 
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: 0.2119
  time to fit residues: 45.2832
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  : 0.707 
-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.093530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.080905 restraints weight = 19695.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.083127 restraints weight = 14778.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.083587 restraints weight = 10537.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6445
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5923  Z= 0.158
  Angle     :  0.605   6.357   8066  Z= 0.319
  Chirality :  0.047   0.179    909
  Planarity :  0.005   0.036   1036
  Dihedral  :  4.495  17.870    779
  Min Nonbonded Distance : 2.506

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: -0.62 (0.32), residues: 262
  loop : -0.80 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  88 
 HIS   0.005   0.001   HIS B 334 
 PHE   0.012   0.001   PHE B 308 
 TYR   0.015   0.002   TYR A 391 
 ARG   0.006   0.001   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  162)
  hydrogen bonds       : angle       7.93913 (  429)
  SS BOND              : bond        0.00378 (   22)
  SS BOND              : angle       1.78611 (   44)
  covalent geometry    : bond        0.00358 ( 5901)
  covalent geometry    : angle       0.59187 ( 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  : 0.730 
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: 0.8186 (mt) cc_final: 0.7478 (mt)
REVERT: E  257 ASP cc_start: 0.8476 (m-30) cc_final: 0.8184 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1934
  time to fit residues: 25.8530
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  : 0.635 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.4980
   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:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 352 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.084922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.070287 restraints weight = 21189.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.072237 restraints weight = 13228.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.073559 restraints weight = 9459.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6546
moved from start:          0.3831

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= 0.149
  Angle     :  0.571   5.713   8066  Z= 0.299
  Chirality :  0.046   0.179    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.494  19.400    779
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.35 %
    Favored  : 95.50 %
  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: -0.80 (0.31), residues: 725
  helix:  0.80 (0.59), residues: 82
  sheet: -0.36 (0.35), residues: 228
  loop : -0.88 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.005   0.001   HIS D 102 
 PHE   0.008   0.001   PHE B 308 
 TYR   0.013   0.002   TYR E 216 
 ARG   0.004   0.000   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  162)
  hydrogen bonds       : angle       7.14240 (  429)
  SS BOND              : bond        0.00470 (   22)
  SS BOND              : angle       1.27889 (   44)
  covalent geometry    : bond        0.00325 ( 5901)
  covalent geometry    : angle       0.56461 ( 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
  95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8266 (mt) cc_final: 0.7607 (mt)
REVERT: A  404 MET cc_start: 0.7569 (mmm) cc_final: 0.7146 (tpp)
REVERT: D  123 MET cc_start: 0.7403 (mmm) cc_final: 0.6997 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 95
  average time/residue: 0.2023
  time to fit residues: 25.5406
Evaluate side-chains
  64 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 366 ASN
B 381 GLN
D  49 GLN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.090111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.077672 restraints weight = 20493.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.078638 restraints weight = 16968.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.079486 restraints weight = 13158.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5923  Z= 0.181
  Angle     :  0.591   5.636   8066  Z= 0.307
  Chirality :  0.046   0.169    909
  Planarity :  0.004   0.036   1036
  Dihedral  :  4.760  18.488    779
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  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: -1.05 (0.31), residues: 725
  helix:  0.52 (0.59), residues: 82
  sheet: -0.53 (0.34), residues: 248
  loop : -1.03 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  88 
 HIS   0.014   0.001   HIS E  68 
 PHE   0.011   0.001   PHE C  44 
 TYR   0.026   0.002   TYR A 306 
 ARG   0.004   0.001   ARG B 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03797 (  162)
  hydrogen bonds       : angle       7.06347 (  429)
  SS BOND              : bond        0.00554 (   22)
  SS BOND              : angle       1.46285 (   44)
  covalent geometry    : bond        0.00409 ( 5901)
  covalent geometry    : angle       0.58229 ( 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
  81 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8340 (mt) cc_final: 0.7629 (mt)
REVERT: D  105 LYS cc_start: 0.7682 (mmtp) cc_final: 0.7297 (pptt)
REVERT: D  123 MET cc_start: 0.7462 (mmm) cc_final: 0.7034 (mmm)
REVERT: D  146 ASN cc_start: 0.8041 (t0) cc_final: 0.7775 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2285
  time to fit residues: 25.6201
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  : 0.844 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  90 HIS
E 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.090624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.077567 restraints weight = 20096.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.078765 restraints weight = 14372.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.080567 restraints weight = 11512.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5923  Z= 0.128
  Angle     :  0.559   6.596   8066  Z= 0.290
  Chirality :  0.046   0.171    909
  Planarity :  0.004   0.036   1036
  Dihedral  :  4.592  17.133    779
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.59 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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: -0.97 (0.31), residues: 725
  helix:  0.65 (0.60), residues: 82
  sheet: -0.60 (0.33), residues: 247
  loop : -0.89 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  88 
 HIS   0.009   0.001   HIS E  68 
 PHE   0.009   0.001   PHE D 133 
 TYR   0.020   0.002   TYR A 306 
 ARG   0.003   0.000   ARG A 352 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  162)
  hydrogen bonds       : angle       6.74302 (  429)
  SS BOND              : bond        0.00311 (   22)
  SS BOND              : angle       1.68632 (   44)
  covalent geometry    : bond        0.00290 ( 5901)
  covalent geometry    : angle       0.54674 ( 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
  79 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8395 (mt) cc_final: 0.7679 (mt)
REVERT: D  105 LYS cc_start: 0.7746 (mmtp) cc_final: 0.7342 (pptt)
REVERT: D  123 MET cc_start: 0.7240 (mmm) cc_final: 0.6829 (mmm)
REVERT: D  146 ASN cc_start: 0.8155 (t0) cc_final: 0.7916 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2803
  time to fit residues: 30.8821
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  : 1.355 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 68 optimal weight:    0.2980
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
E 327 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.091211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.078476 restraints weight = 19967.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.079120 restraints weight = 14418.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.081044 restraints weight = 12230.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.4746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5923  Z= 0.118
  Angle     :  0.537   5.156   8066  Z= 0.278
  Chirality :  0.045   0.167    909
  Planarity :  0.004   0.053   1036
  Dihedral  :  4.486  17.608    779
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.17 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  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: -0.94 (0.31), residues: 725
  helix:  0.70 (0.61), residues: 81
  sheet: -0.58 (0.33), residues: 245
  loop : -0.88 (0.31), residues: 399

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   0.009   0.001   PHE D 133 
 TYR   0.017   0.002   TYR A 306 
 ARG   0.013   0.001   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  162)
  hydrogen bonds       : angle       6.64756 (  429)
  SS BOND              : bond        0.00287 (   22)
  SS BOND              : angle       1.33347 (   44)
  covalent geometry    : bond        0.00269 ( 5901)
  covalent geometry    : angle       0.52908 ( 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
  81 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.736 
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: 0.7696 (mt)
REVERT: D  105 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7326 (pptt)
REVERT: D  123 MET cc_start: 0.7167 (mmm) cc_final: 0.6808 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1767
  time to fit residues: 19.6261
Evaluate side-chains
  65 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.090853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.077481 restraints weight = 20224.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.078868 restraints weight = 14758.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.080709 restraints weight = 12049.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5923  Z= 0.130
  Angle     :  0.556   6.754   8066  Z= 0.286
  Chirality :  0.045   0.163    909
  Planarity :  0.004   0.037   1036
  Dihedral  :  4.603  19.344    779
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.28 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  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: -1.09 (0.31), residues: 725
  helix:  0.28 (0.58), residues: 87
  sheet: -0.63 (0.32), residues: 253
  loop : -0.96 (0.31), residues: 385

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 C  44 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.008   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03285 (  162)
  hydrogen bonds       : angle       6.60390 (  429)
  SS BOND              : bond        0.00350 (   22)
  SS BOND              : angle       1.53990 (   44)
  covalent geometry    : bond        0.00291 ( 5901)
  covalent geometry    : angle       0.54614 ( 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  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8377 (mt) cc_final: 0.7671 (mt)
REVERT: D  105 LYS cc_start: 0.7766 (mmtp) cc_final: 0.7400 (pptt)
REVERT: D  123 MET cc_start: 0.7312 (mmm) cc_final: 0.6905 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1761
  time to fit residues: 17.3485
Evaluate side-chains
  57 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0670
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.9722

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

Flipped N/Q/H residues before XYZ refinement:
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  40 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.090323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.077315 restraints weight = 20109.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.078348 restraints weight = 14446.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.080013 restraints weight = 12293.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.5091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5923  Z= 0.137
  Angle     :  0.578   7.915   8066  Z= 0.296
  Chirality :  0.046   0.161    909
  Planarity :  0.004   0.035   1036
  Dihedral  :  4.643  19.012    779
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  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: -1.08 (0.31), residues: 725
  helix: -0.02 (0.57), residues: 92
  sheet: -0.58 (0.34), residues: 236
  loop : -0.91 (0.31), residues: 397

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   0.008   0.001   PHE B 308 
 TYR   0.016   0.002   TYR A 339 
 ARG   0.007   0.001   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03282 (  162)
  hydrogen bonds       : angle       6.51638 (  429)
  SS BOND              : bond        0.00370 (   22)
  SS BOND              : angle       1.80130 (   44)
  covalent geometry    : bond        0.00310 ( 5901)
  covalent geometry    : angle       0.56381 ( 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
  75 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8338 (mt) cc_final: 0.7575 (tp)
REVERT: D  105 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7443 (pptt)
REVERT: D  123 MET cc_start: 0.7301 (mmm) cc_final: 0.6951 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1696
  time to fit residues: 18.2439
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  : 1.302 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 25 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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**
** E  40 HIS ** 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 = 0.4034 r_free = 0.4034 target = 0.089898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.077052 restraints weight = 20335.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.078178 restraints weight = 15149.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.079363 restraints weight = 12355.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6592
moved from start:          0.5244

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= 0.129
  Angle     :  0.560   7.917   8066  Z= 0.288
  Chirality :  0.046   0.157    909
  Planarity :  0.004   0.036   1036
  Dihedral  :  4.612  19.329    779
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.41 %
    Favored  : 95.45 %
  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: -1.05 (0.31), residues: 725
  helix: -0.02 (0.57), residues: 92
  sheet: -0.59 (0.35), residues: 215
  loop : -0.87 (0.30), residues: 418

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 C  44 
 TYR   0.017   0.002   TYR A 306 
 ARG   0.006   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  162)
  hydrogen bonds       : angle       6.46300 (  429)
  SS BOND              : bond        0.00344 (   22)
  SS BOND              : angle       1.78305 (   44)
  covalent geometry    : bond        0.00292 ( 5901)
  covalent geometry    : angle       0.54596 ( 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
  74 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8330 (mt) cc_final: 0.7461 (tp)
REVERT: D  105 LYS cc_start: 0.7803 (mmtp) cc_final: 0.7504 (pptt)
REVERT: D  123 MET cc_start: 0.7344 (mmm) cc_final: 0.7056 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1733
  time to fit residues: 17.6676
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  : 0.661 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0060
   chunk 14 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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**
** E  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  71 ASN
E 169 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.091228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.078349 restraints weight = 20135.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.079904 restraints weight = 14761.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.081448 restraints weight = 10705.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.5403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5923  Z= 0.102
  Angle     :  0.540   8.239   8066  Z= 0.276
  Chirality :  0.045   0.158    909
  Planarity :  0.004   0.036   1036
  Dihedral  :  4.403  17.883    779
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.45 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    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: -1.07 (0.31), residues: 725
  helix:  0.02 (0.57), residues: 92
  sheet: -0.62 (0.34), residues: 225
  loop : -0.88 (0.30), residues: 408

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  53 
 TYR   0.017   0.001   TYR A 306 
 ARG   0.006   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03024 (  162)
  hydrogen bonds       : angle       6.29659 (  429)
  SS BOND              : bond        0.00267 (   22)
  SS BOND              : angle       1.61137 (   44)
  covalent geometry    : bond        0.00230 ( 5901)
  covalent geometry    : angle       0.52833 ( 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
  77 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 LEU cc_start: 0.8308 (mt) cc_final: 0.7680 (mt)
REVERT: D  123 MET cc_start: 0.7297 (mmm) cc_final: 0.7032 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1470
  time to fit residues: 16.0241
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  : 0.711 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0670
   chunk 54 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5016

-------------------------------------------------------------------------------
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**
** E  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 109 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 = 0.4063 r_free = 0.4063 target = 0.091342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.078695 restraints weight = 20253.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.080249 restraints weight = 13946.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.081145 restraints weight = 11854.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5923  Z= 0.105
  Angle     :  0.548   8.118   8066  Z= 0.281
  Chirality :  0.046   0.153    909
  Planarity :  0.004   0.036   1036
  Dihedral  :  4.464  24.369    779
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.45 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.06 (0.31), residues: 725
  helix:  0.06 (0.57), residues: 92
  sheet: -0.58 (0.34), residues: 225
  loop : -0.91 (0.30), residues: 408

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   0.008   0.001   PHE D  53 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.006   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03014 (  162)
  hydrogen bonds       : angle       6.22872 (  429)
  SS BOND              : bond        0.00267 (   22)
  SS BOND              : angle       1.58483 (   44)
  covalent geometry    : bond        0.00236 ( 5901)
  covalent geometry    : angle       0.53644 ( 8022)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2522.74 seconds
wall clock time: 46 minutes 3.44 seconds (2763.44 seconds total)