Starting phenix.real_space_refine
on Thu Feb  5 00:15:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o98_70245/02_2026/9o98_70245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o98_70245/02_2026/9o98_70245.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o98_70245/02_2026/9o98_70245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o98_70245/02_2026/9o98_70245.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o98_70245/02_2026/9o98_70245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o98_70245/02_2026/9o98_70245.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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: 6
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      4      4.86       5
     C    4374      2.51       5
     N    1118      2.21       5
     O    1126      1.98       5
     H    6954      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13616
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 6806
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 19, 'TRANS': 424}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.33, per 1000 atoms: 0.46
  Number of scatterers: 13616
  At special positions: 0
  Unit cell: (80.028, 110.808, 75.924, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      4     17.00
     S      40     16.00
     O    1126      8.00
     N    1118      7.00
     C    4374      6.00
     H    6954      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 409.7 milliseconds
  

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      83.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 26
      removed outlier: 3.575A  pdb=" N   LEU A  26 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 68
      removed outlier: 3.595A  pdb=" N   LEU A  36 " --> pdb=" O   PRO A  32 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL A  41 " --> pdb=" O   PHE A  37 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU A  68 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.904A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 105
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.773A  pdb=" N   ILE A 112 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 140
      Proline residue:  A 129  - end of helix
      removed outlier: 3.685A  pdb=" N   GLY A 135 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 167
    Processing helix  chain 'A' and resid 170 through 191
      removed outlier: 3.641A  pdb=" N   ARG A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 203
      removed outlier: 3.756A  pdb=" N   ILE A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 232
      removed outlier: 3.513A  pdb=" N   VAL A 218 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 250
      No H-bonds generated for 'chain 'A' and resid 248 through 250'
    Processing helix  chain 'A' and resid 251 through 285
      removed outlier: 3.965A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.545A  pdb=" N   GLN A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 279 " --> pdb=" O   GLY A 275 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
    Processing helix  chain 'A' and resid 310 through 313
      removed outlier: 3.653A  pdb=" N   SER A 313 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 310 through 313'
    Processing helix  chain 'A' and resid 319 through 325
    Processing helix  chain 'A' and resid 329 through 350
      removed outlier: 3.761A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA A 339 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.800A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
    Processing helix  chain 'A' and resid 386 through 394
    Processing helix  chain 'A' and resid 395 through 402
      removed outlier: 3.742A  pdb=" N   ALA A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 417
    Processing helix  chain 'A' and resid 421 through 440
      removed outlier: 3.646A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 4.039A  pdb=" N   GLU A 459 " --> pdb=" O   LYS A 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 26
      removed outlier: 3.574A  pdb=" N   LEU B  26 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 68
      removed outlier: 3.594A  pdb=" N   LEU B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL B  41 " --> pdb=" O   PHE B  37 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU B  68 " --> pdb=" O   ARG B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.905A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 105
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 3.773A  pdb=" N   ILE B 112 " --> pdb=" O   GLY B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 140
      Proline residue:  B 129  - end of helix
      removed outlier: 3.684A  pdb=" N   GLY B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 167
    Processing helix  chain 'B' and resid 170 through 191
      removed outlier: 3.641A  pdb=" N   ARG B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
      removed outlier: 3.756A  pdb=" N   ILE B 197 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 232
      removed outlier: 3.513A  pdb=" N   VAL B 218 " --> pdb=" O   SER B 214 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 250
      No H-bonds generated for 'chain 'B' and resid 248 through 250'
    Processing helix  chain 'B' and resid 251 through 285
      removed outlier: 3.965A  pdb=" N   TYR B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU B 258 " --> pdb=" O   LEU B 254 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.544A  pdb=" N   GLN B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU B 279 " --> pdb=" O   GLY B 275 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG B 282 " --> pdb=" O   ASP B 278 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   HIS B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 309
    Processing helix  chain 'B' and resid 310 through 313
      removed outlier: 3.654A  pdb=" N   SER B 313 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 313'
    Processing helix  chain 'B' and resid 319 through 325
    Processing helix  chain 'B' and resid 329 through 350
      removed outlier: 3.761A  pdb=" N   PHE B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER B 350 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 3.799A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
    Processing helix  chain 'B' and resid 386 through 394
    Processing helix  chain 'B' and resid 395 through 402
      removed outlier: 3.742A  pdb=" N   ALA B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 421 through 440
      removed outlier: 3.502A  pdb=" N   MET B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 459
      removed outlier: 4.039A  pdb=" N   GLU B 459 " --> pdb=" O   LYS B 455 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1437 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.78

  Time building geometry restraints manager: 1.71 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6948
        1.03 -     1.23: 9
        1.23 -     1.42: 2733
        1.42 -     1.61: 3992
        1.61 -     1.81: 74
  Bond restraints: 13756
  Sorted by residual:
  bond pdb=" N   ARG B  17 "
       pdb=" CA  ARG B  17 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  bond pdb=" N   ARG A  17 "
       pdb=" CA  ARG A  17 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.81e+00
  bond pdb=" C   ARG B 205 "
       pdb=" N   PRO B 206 "
    ideal  model  delta    sigma   weight residual
    1.330  1.350 -0.019 1.19e-02 7.06e+03 2.65e+00
  bond pdb=" N   ARG B  17 "
       pdb=" H   ARG B  17 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.35e+00
  bond pdb=" C   ARG A 205 "
       pdb=" N   PRO A 206 "
    ideal  model  delta    sigma   weight residual
    1.331  1.350 -0.018 1.20e-02 6.94e+03 2.34e+00
  ... (remaining 13751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 22099
        0.92 -     1.84: 2730
        1.84 -     2.76: 96
        2.76 -     3.68: 41
        3.68 -     4.60: 14
  Bond angle restraints: 24980
  Sorted by residual:
  angle pdb=" N   VAL A 374 "
        pdb=" CA  VAL A 374 "
        pdb=" C   VAL A 374 "
      ideal   model   delta    sigma   weight residual
     112.96  108.71    4.25 1.00e+00 1.00e+00 1.80e+01
  angle pdb=" N   VAL B 374 "
        pdb=" CA  VAL B 374 "
        pdb=" C   VAL B 374 "
      ideal   model   delta    sigma   weight residual
     112.96  108.77    4.19 1.00e+00 1.00e+00 1.75e+01
  angle pdb=" CA  GLY A 314 "
        pdb=" C   GLY A 314 "
        pdb=" O   GLY A 314 "
      ideal   model   delta    sigma   weight residual
     122.57  120.42    2.15 9.20e-01 1.18e+00 5.47e+00
  angle pdb=" CA  GLY B 354 "
        pdb=" C   GLY B 354 "
        pdb=" N   GLY B 355 "
      ideal   model   delta    sigma   weight residual
     114.86  117.17   -2.31 1.01e+00 9.80e-01 5.24e+00
  angle pdb=" CA  GLY B 314 "
        pdb=" C   GLY B 314 "
        pdb=" O   GLY B 314 "
      ideal   model   delta    sigma   weight residual
     122.57  120.47    2.10 9.20e-01 1.18e+00 5.21e+00
  ... (remaining 24975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 5665
       16.92 -    33.84: 413
       33.84 -    50.77: 176
       50.77 -    67.69: 110
       67.69 -    84.61: 28
  Dihedral angle restraints: 6392
    sinusoidal: 3490
      harmonic: 2902
  Sorted by residual:
  dihedral pdb=" CA  LYS B  99 "
           pdb=" C   LYS B  99 "
           pdb=" N   TYR B 100 "
           pdb=" CA  TYR B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.72  -16.28     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  LYS A  99 "
           pdb=" C   LYS A  99 "
           pdb=" N   TYR A 100 "
           pdb=" CA  TYR A 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.78  -16.22     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CG  ARG B 160 "
           pdb=" CD  ARG B 160 "
           pdb=" NE  ARG B 160 "
           pdb=" CZ  ARG B 160 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.02   43.02     2      1.50e+01 4.44e-03 9.93e+00
  ... (remaining 6389 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 619
       0.024 -    0.047: 251
       0.047 -    0.071: 147
       0.071 -    0.094: 49
       0.094 -    0.118: 20
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CA  ILE B 239 "
            pdb=" N   ILE B 239 "
            pdb=" C   ILE B 239 "
            pdb=" CB  ILE B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.46e-01
  chirality pdb=" CA  ILE A 239 "
            pdb=" N   ILE A 239 "
            pdb=" C   ILE A 239 "
            pdb=" CB  ILE A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.33e-01
  chirality pdb=" CA  ILE B 213 "
            pdb=" N   ILE B 213 "
            pdb=" C   ILE B 213 "
            pdb=" CB  ILE B 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.32e-01
  ... (remaining 1083 not shown)

  Planarity restraints: 2008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 267 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 266 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO A 267 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 417 "   -0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   ASP B 417 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ASP B 417 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN B 418 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2005 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 2422
        2.30 -     2.88: 30337
        2.88 -     3.45: 33345
        3.45 -     4.03: 45508
        4.03 -     4.60: 71550
  Nonbonded interactions: 183162
  Sorted by model distance:
  nonbonded pdb=" HG  SER A  86 "
            pdb=" O   GLY A 141 "
     model   vdw
     1.728 2.450
  nonbonded pdb=" HG  SER B  86 "
            pdb=" O   GLY B 141 "
     model   vdw
     1.728 2.450
  nonbonded pdb=" OE1 GLU A 414 "
            pdb=" HH  TYR B 419 "
     model   vdw
     1.753 2.450
  nonbonded pdb=" HH  TYR A 419 "
            pdb=" OE1 GLU B 414 "
     model   vdw
     1.753 2.450
  nonbonded pdb=" OD1 ASP B 171 "
            pdb="HH11 ARG B 174 "
     model   vdw
     1.849 2.450
  ... (remaining 183157 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.800
  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:             0.090
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     17.160
  Find NCS groups from input model:        0.060
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
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   0.032   6802  Z= 0.150
  Angle     :  0.541   4.246   9234  Z= 0.329
  Chirality :  0.036   0.118   1086
  Planarity :  0.005   0.040   1160
  Dihedral  : 13.206  80.338   2396
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  3.89 %
    Favored  : 95.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.30), residues: 884
  helix:  1.56 (0.22), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.29 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 160 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.009   0.001   PHE A  53 
 TRP   0.009   0.001   TRP B 253 
 HIS   0.003   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6802)
  covalent geometry    : angle       0.54132 ( 9234)
  hydrogen bonds       : bond        0.18751 (  483)
  hydrogen bonds       : angle       6.37900 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7615 (mtm-85)
REVERT: A  332 MET cc_start: 0.7429 (tpt) cc_final: 0.7188 (tpp)
  outliers start: 4
  outliers final: 4
  residues processed: 66
  average time/residue: 0.1964
  time to fit residues: 17.3638
Evaluate side-chains
  62 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  201 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   overall best weight:    1.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.128543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.111439 restraints weight = 23593.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.57
r_work: 0.3173 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6802  Z= 0.170
  Angle     :  0.511   4.264   9234  Z= 0.280
  Chirality :  0.038   0.117   1086
  Planarity :  0.005   0.042   1160
  Dihedral  :  4.745  37.386    956
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  5.99 %
    Favored  : 93.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.29), residues: 884
  helix:  2.10 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.99 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 160 
 TYR   0.009   0.001   TYR B 419 
 PHE   0.009   0.001   PHE B 190 
 TRP   0.009   0.001   TRP B 253 
 HIS   0.003   0.001   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6802)
  covalent geometry    : angle       0.51096 ( 9234)
  hydrogen bonds       : bond        0.07524 (  483)
  hydrogen bonds       : angle       4.23890 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 ARG cc_start: 0.8387 (mtp180) cc_final: 0.7540 (mtm-85)
REVERT: A  332 MET cc_start: 0.7540 (tpt) cc_final: 0.7278 (tpp)
REVERT: B  282 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7376 (mtm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 67
  average time/residue: 0.1729
  time to fit residues: 15.6560
Evaluate side-chains
  65 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 ASP
Chi-restraints excluded: chain A residue  294 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0970
   chunk 59 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.122437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.103615 restraints weight = 23320.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.66
r_work: 0.3073 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6802  Z= 0.112
  Angle     :  0.437   4.159   9234  Z= 0.235
  Chirality :  0.036   0.118   1086
  Planarity :  0.005   0.039   1160
  Dihedral  :  3.638  13.757    946
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  7.63 %
    Favored  : 92.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.29), residues: 884
  helix:  2.53 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.96 (0.33), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 160 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.007   0.001   PHE B 190 
 TRP   0.009   0.001   TRP B 253 
 HIS   0.002   0.001   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6802)
  covalent geometry    : angle       0.43728 ( 9234)
  hydrogen bonds       : bond        0.05671 (  483)
  hydrogen bonds       : angle       3.87580 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 ARG cc_start: 0.8351 (mtp180) cc_final: 0.7485 (mtm-85)
REVERT: A  332 MET cc_start: 0.7354 (tpt) cc_final: 0.7078 (tpp)
REVERT: B  282 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7301 (mtm-85)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1873
  time to fit residues: 15.9103
Evaluate side-chains
  61 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 84 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.121977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.103206 restraints weight = 23201.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.66
r_work: 0.3034 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6802  Z= 0.119
  Angle     :  0.437   4.088   9234  Z= 0.233
  Chirality :  0.036   0.120   1086
  Planarity :  0.005   0.040   1160
  Dihedral  :  3.552  13.499    946
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.19 %
    Favored  : 91.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.36 (0.29), residues: 884
  helix:  2.66 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -2.12 (0.34), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  18 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.008   0.001   PHE B  53 
 TRP   0.008   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6802)
  covalent geometry    : angle       0.43686 ( 9234)
  hydrogen bonds       : bond        0.05598 (  483)
  hydrogen bonds       : angle       3.77672 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7443 (mtm-85)
REVERT: A  332 MET cc_start: 0.7317 (tpt) cc_final: 0.7028 (tpp)
REVERT: B  282 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7312 (mtm-85)
  outliers start: 7
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1912
  time to fit residues: 16.6194
Evaluate side-chains
  61 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0870
   chunk 62 optimal weight:    0.4980
   chunk 86 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6560

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.123431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.104574 restraints weight = 23220.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.68
r_work: 0.3051 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6802  Z= 0.104
  Angle     :  0.417   4.104   9234  Z= 0.221
  Chirality :  0.035   0.119   1086
  Planarity :  0.005   0.039   1160
  Dihedral  :  3.452  13.491    946
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.38 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.29), residues: 884
  helix:  2.82 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.07 (0.34), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 160 
 TYR   0.006   0.001   TYR B 419 
 PHE   0.007   0.001   PHE B  53 
 TRP   0.008   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 6802)
  covalent geometry    : angle       0.41675 ( 9234)
  hydrogen bonds       : bond        0.05006 (  483)
  hydrogen bonds       : angle       3.66697 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7421 (mtm-85)
REVERT: A  332 MET cc_start: 0.7294 (tpt) cc_final: 0.6998 (tpp)
REVERT: A  417 ASP cc_start: 0.7106 (t0) cc_final: 0.6885 (t0)
REVERT: B  123 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7416 (mtm180)
REVERT: B  282 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7301 (mtm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 67
  average time/residue: 0.2062
  time to fit residues: 18.1007
Evaluate side-chains
  62 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    0.1980
   chunk 65 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0070
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.5598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.124291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.105671 restraints weight = 22997.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.65
r_work: 0.3067 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6802  Z= 0.099
  Angle     :  0.409   4.032   9234  Z= 0.216
  Chirality :  0.035   0.119   1086
  Planarity :  0.004   0.039   1160
  Dihedral  :  3.365  13.417    946
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.63 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.30), residues: 884
  helix:  2.94 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.02 (0.36), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 160 
 TYR   0.006   0.001   TYR B 419 
 PHE   0.007   0.001   PHE B  53 
 TRP   0.007   0.001   TRP A 253 
 HIS   0.002   0.000   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 6802)
  covalent geometry    : angle       0.40947 ( 9234)
  hydrogen bonds       : bond        0.04676 (  483)
  hydrogen bonds       : angle       3.58551 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7419 (mtm-85)
REVERT: A  332 MET cc_start: 0.7318 (tpt) cc_final: 0.7019 (tpp)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1813
  time to fit residues: 16.0798
Evaluate side-chains
  63 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.132581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.116125 restraints weight = 23122.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.55
r_work: 0.3189 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6802  Z= 0.141
  Angle     :  0.448   4.036   9234  Z= 0.240
  Chirality :  0.036   0.122   1086
  Planarity :  0.005   0.042   1160
  Dihedral  :  3.442  13.169    946
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.23 %
    Favored  : 91.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.29), residues: 884
  helix:  2.77 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -2.27 (0.34), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.010   0.001   PHE B  53 
 TRP   0.010   0.001   TRP B 253 
 HIS   0.003   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6802)
  covalent geometry    : angle       0.44815 ( 9234)
  hydrogen bonds       : bond        0.05985 (  483)
  hydrogen bonds       : angle       3.73637 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7664 (mpt180) cc_final: 0.6725 (ttp-170)
REVERT: A  282 ARG cc_start: 0.8318 (mtp180) cc_final: 0.7481 (mtm-85)
REVERT: A  332 MET cc_start: 0.7567 (tpt) cc_final: 0.7294 (tpp)
REVERT: A  417 ASP cc_start: 0.7298 (t0) cc_final: 0.7076 (t0)
REVERT: B  330 MET cc_start: 0.8030 (mmm) cc_final: 0.7436 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 70
  average time/residue: 0.2195
  time to fit residues: 19.8264
Evaluate side-chains
  67 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 53 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.122111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.103644 restraints weight = 23144.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.65
r_work: 0.3041 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6802  Z= 0.108
  Angle     :  0.420   4.018   9234  Z= 0.223
  Chirality :  0.035   0.120   1086
  Planarity :  0.005   0.041   1160
  Dihedral  :  3.406  13.421    946
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.53 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.29), residues: 884
  helix:  2.88 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.14 (0.35), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 160 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.008   0.001   PHE B  53 
 TRP   0.008   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6802)
  covalent geometry    : angle       0.42037 ( 9234)
  hydrogen bonds       : bond        0.05179 (  483)
  hydrogen bonds       : angle       3.64911 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 ARG cc_start: 0.7430 (mpt180) cc_final: 0.6503 (ttp-170)
REVERT: A  282 ARG cc_start: 0.8273 (mtp180) cc_final: 0.7398 (mtm-85)
REVERT: A  417 ASP cc_start: 0.7192 (t0) cc_final: 0.6955 (t0)
REVERT: B  330 MET cc_start: 0.7978 (mmm) cc_final: 0.7340 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 0.2066
  time to fit residues: 17.3175
Evaluate side-chains
  63 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.121641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.102920 restraints weight = 23406.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.69
r_work: 0.3022 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6802  Z= 0.121
  Angle     :  0.429   3.997   9234  Z= 0.228
  Chirality :  0.036   0.122   1086
  Planarity :  0.005   0.042   1160
  Dihedral  :  3.406  13.386    946
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.68 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.29), residues: 884
  helix:  2.82 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.17 (0.35), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.007   0.001   TYR B 419 
 PHE   0.009   0.001   PHE B  53 
 TRP   0.009   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6802)
  covalent geometry    : angle       0.42883 ( 9234)
  hydrogen bonds       : bond        0.05492 (  483)
  hydrogen bonds       : angle       3.68161 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7419 (mpt180) cc_final: 0.6472 (ttp-170)
REVERT: A  282 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7374 (mtm-85)
REVERT: A  417 ASP cc_start: 0.7171 (t0) cc_final: 0.6923 (t0)
REVERT: B  330 MET cc_start: 0.7983 (mmm) cc_final: 0.7359 (mmt)
  outliers start: 5
  outliers final: 5
  residues processed: 67
  average time/residue: 0.1927
  time to fit residues: 17.5492
Evaluate side-chains
  65 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.128617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.112216 restraints weight = 23577.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.54
r_work: 0.3163 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6802  Z= 0.178
  Angle     :  0.489   4.171   9234  Z= 0.263
  Chirality :  0.038   0.125   1086
  Planarity :  0.005   0.043   1160
  Dihedral  :  3.564  13.219    946
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.98 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.29), residues: 884
  helix:  2.56 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -2.37 (0.34), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 209 
 TYR   0.009   0.001   TYR A 419 
 PHE   0.014   0.002   PHE B  53 
 TRP   0.011   0.001   TRP B 253 
 HIS   0.004   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6802)
  covalent geometry    : angle       0.48900 ( 9234)
  hydrogen bonds       : bond        0.06859 (  483)
  hydrogen bonds       : angle       3.86101 ( 1437)

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7652 (mpt180) cc_final: 0.6725 (ttp-170)
REVERT: A  282 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7450 (mtm-85)
REVERT: A  417 ASP cc_start: 0.7303 (t0) cc_final: 0.7049 (t0)
REVERT: B   62 ASN cc_start: 0.6948 (m-40) cc_final: 0.6737 (m-40)
  outliers start: 5
  outliers final: 5
  residues processed: 66
  average time/residue: 0.2146
  time to fit residues: 18.8166
Evaluate side-chains
  66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.121888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.103408 restraints weight = 23194.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.65
r_work: 0.3031 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6802  Z= 0.109
  Angle     :  0.423   4.017   9234  Z= 0.225
  Chirality :  0.035   0.120   1086
  Planarity :  0.005   0.043   1160
  Dihedral  :  3.463  13.676    946
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.83 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.29), residues: 884
  helix:  2.80 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.17 (0.35), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  18 
 TYR   0.006   0.001   TYR B 419 
 PHE   0.007   0.001   PHE A 190 
 TRP   0.008   0.001   TRP B 253 
 HIS   0.002   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6802)
  covalent geometry    : angle       0.42299 ( 9234)
  hydrogen bonds       : bond        0.05262 (  483)
  hydrogen bonds       : angle       3.68469 ( 1437)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2975.57 seconds
wall clock time: 51 minutes 8.37 seconds (3068.37 seconds total)