Starting phenix.real_space_refine
on Wed Feb  4 23:59:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o96_70243/02_2026/9o96_70243.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o96_70243/02_2026/9o96_70243.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o96_70243/02_2026/9o96_70243.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o96_70243/02_2026/9o96_70243.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o96_70243/02_2026/9o96_70243.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o96_70243/02_2026/9o96_70243.cif"
  }
  resolution = 3.2
  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=   0.003 sd=   0.035
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    4380      2.51       5
     N    1120      2.21       5
     O    1126      1.98       5
     H    6970      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 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: 13640
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 6818
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 19, 'TRANS': 424}
    Chain: "B"
      Number of atoms: 6818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 444, 6818
          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}
    Chain: "B"
      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}
  Time building chain proxies: 2.66, per 1000 atoms: 0.20
  Number of scatterers: 13640
  At special positions: 0
  Unit cell: (109.728, 111.456, 73.44, 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    1120      7.00
     C    4380      6.00
     H    6970      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: 1.01
  Conformation dependent library (CDL) restraints added in 451.2 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:
      50 helices and 0 sheets defined
      86.0% 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 19
      No H-bonds generated for 'chain 'A' and resid 17 through 19'
    Processing helix  chain 'A' and resid 20 through 68
      removed outlier: 3.618A  pdb=" N   GLN A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ARG A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   THR A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      Proline residue:  A  32  - end of helix
      removed outlier: 4.016A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A  41 " --> pdb=" O   PHE A  37 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.750A  pdb=" N   LEU A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A  92 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG A  98 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 105
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.525A  pdb=" N   GLU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 141
      Proline residue:  A 129  - end of helix
      removed outlier: 3.675A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 167
      removed outlier: 3.540A  pdb=" N   VAL A 162 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 191
      removed outlier: 3.658A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 179 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A 189 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 203
      removed outlier: 3.506A  pdb=" N   GLY A 196 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 232
      removed outlier: 3.531A  pdb=" N   ILE A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 251
    Processing helix  chain 'A' and resid 252 through 285
      removed outlier: 3.891A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A 265 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.850A  pdb=" N   GLN A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 279 " --> pdb=" O   GLY A 275 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ARG A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   VAL A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
      removed outlier: 3.550A  pdb=" N   CYS A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 313
    Processing helix  chain 'A' and resid 315 through 318
      removed outlier: 3.634A  pdb=" N   ASN A 318 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 315 through 318'
    Processing helix  chain 'A' and resid 319 through 325
    Processing helix  chain 'A' and resid 329 through 350
      removed outlier: 3.945A  pdb=" N   VAL A 334 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.850A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.746A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 386 through 393
      removed outlier: 3.516A  pdb=" N   ALA A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 402
    Processing helix  chain 'A' and resid 404 through 417
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 439
      removed outlier: 3.694A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLN A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 457
      removed outlier: 3.966A  pdb=" N   LYS A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 19
      No H-bonds generated for 'chain 'B' and resid 17 through 19'
    Processing helix  chain 'B' and resid 20 through 68
      removed outlier: 3.719A  pdb=" N   GLN B  24 " --> pdb=" O   GLN B  20 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ARG B  28 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   THR B  31 " --> pdb=" O   GLU B  27 " (cutoff:3.500A)
      Proline residue:  B  32  - end of helix
      removed outlier: 4.068A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL B  41 " --> pdb=" O   PHE B  37 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.822A  pdb=" N   LEU B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 3.639A  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
    Processing helix  chain 'B' and resid 123 through 141
      Proline residue:  B 129  - end of helix
      removed outlier: 3.532A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 167
      removed outlier: 3.538A  pdb=" N   VAL B 162 " --> pdb=" O   ILE B 158 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 191
      removed outlier: 3.658A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA B 188 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA B 189 " --> pdb=" O   GLY B 185 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
      removed outlier: 4.190A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 232
      removed outlier: 4.077A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 251
    Processing helix  chain 'B' and resid 252 through 285
      removed outlier: 3.898A  pdb=" N   LEU B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE B 265 " --> pdb=" O   ILE B 261 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.915A  pdb=" N   GLN B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 279 " --> pdb=" O   GLY B 275 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   ARG B 282 " --> pdb=" O   ASP B 278 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   HIS B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 309
      removed outlier: 3.536A  pdb=" N   CYS B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 313
    Processing helix  chain 'B' and resid 315 through 318
      removed outlier: 3.665A  pdb=" N   ASN B 318 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 315 through 318'
    Processing helix  chain 'B' and resid 319 through 325
    Processing helix  chain 'B' and resid 329 through 350
      removed outlier: 3.932A  pdb=" N   VAL B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU B 346 " --> pdb=" O   ILE B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 3.797A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
      removed outlier: 3.772A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 380 through 383'
    Processing helix  chain 'B' and resid 386 through 393
      removed outlier: 3.550A  pdb=" N   ALA B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 402
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 418 through 420
      No H-bonds generated for 'chain 'B' and resid 418 through 420'
    Processing helix  chain 'B' and resid 421 through 439
      removed outlier: 3.681A  pdb=" N   THR B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN B 437 " --> pdb=" O   THR B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 457
      removed outlier: 3.911A  pdb=" N   LYS B 455 " --> pdb=" O   ARG B 451 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1359 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: 2.86

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        0.95 -     1.13: 6964
        1.13 -     1.30: 1086
        1.30 -     1.47: 2394
        1.47 -     1.65: 3262
        1.65 -     1.82: 74
  Bond restraints: 13780
  Sorted by residual:
  bond pdb=" N   LEU B  33 "
       pdb=" H   LEU B  33 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CE2 TYR A 255 "
       pdb=" HE2 TYR A 255 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   ILE A 391 "
       pdb=" H   ILE A 391 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   PHE A 166 "
       pdb=" H   PHE A 166 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" NH2 ARG B 451 "
       pdb="HH22 ARG B 451 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 13775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 20456
        2.39 -     4.78: 3635
        4.78 -     7.17: 805
        7.17 -     9.56: 126
        9.56 -    11.95: 6
  Bond angle restraints: 25028
  Sorted by residual:
  angle pdb=" CA  PHE A 357 "
        pdb=" CB  PHE A 357 "
        pdb=" CG  PHE A 357 "
      ideal   model   delta    sigma   weight residual
     113.80  121.09   -7.29 1.00e+00 1.00e+00 5.32e+01
  angle pdb=" CA  PHE B 357 "
        pdb=" CB  PHE B 357 "
        pdb=" CG  PHE B 357 "
      ideal   model   delta    sigma   weight residual
     113.80  120.45   -6.65 1.00e+00 1.00e+00 4.42e+01
  angle pdb=" C   LEU B 319 "
        pdb=" N   ILE B 320 "
        pdb=" CA  ILE B 320 "
      ideal   model   delta    sigma   weight residual
     120.33  124.27   -3.94 8.00e-01 1.56e+00 2.42e+01
  angle pdb=" C   ARG A 209 "
        pdb=" N   TYR A 210 "
        pdb=" CA  TYR A 210 "
      ideal   model   delta    sigma   weight residual
     120.71  127.52   -6.81 1.42e+00 4.96e-01 2.30e+01
  angle pdb=" C   ARG B 209 "
        pdb=" N   TYR B 210 "
        pdb=" CA  TYR B 210 "
      ideal   model   delta    sigma   weight residual
     120.71  127.48   -6.77 1.42e+00 4.96e-01 2.27e+01
  ... (remaining 25023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.70: 5818
       16.70 -    33.40: 253
       33.40 -    50.10: 141
       50.10 -    66.80: 182
       66.80 -    83.49: 6
  Dihedral angle restraints: 6400
    sinusoidal: 3498
      harmonic: 2902
  Sorted by residual:
  dihedral pdb=" C   GLU B 459 "
           pdb=" N   GLU B 459 "
           pdb=" CA  GLU B 459 "
           pdb=" CB  GLU B 459 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.99   12.39     0      2.50e+00 1.60e-01 2.46e+01
  dihedral pdb=" C   GLU A 459 "
           pdb=" N   GLU A 459 "
           pdb=" CA  GLU A 459 "
           pdb=" CB  GLU A 459 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.72   12.12     0      2.50e+00 1.60e-01 2.35e+01
  dihedral pdb=" CA  GLN A 207 "
           pdb=" C   GLN A 207 "
           pdb=" N   PHE A 208 "
           pdb=" CA  PHE A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 6397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 715
       0.082 -    0.164: 309
       0.164 -    0.245: 48
       0.245 -    0.327: 12
       0.327 -    0.409: 2
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CA  GLU B 459 "
            pdb=" N   GLU B 459 "
            pdb=" C   GLU B 459 "
            pdb=" CB  GLU B 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" CA  GLU A 459 "
            pdb=" N   GLU A 459 "
            pdb=" C   GLU A 459 "
            pdb=" CB  GLU A 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.89e+00
  chirality pdb=" CA  LYS A 455 "
            pdb=" N   LYS A 455 "
            pdb=" C   LYS A 455 "
            pdb=" CB  LYS A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1083 not shown)

  Planarity restraints: 2008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 125 "   -0.115 2.00e-02 2.50e+03   4.95e-02 9.80e+01
        pdb=" CG  TRP B 125 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 125 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 125 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 125 "    0.033 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 125 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 125 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 125 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 125 "    0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 125 "   -0.034 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 125 "    0.019 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 125 "    0.087 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 125 "    0.082 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 125 "   -0.043 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 125 "    0.045 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 125 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 147 "   -0.355 9.50e-02 1.11e+02   1.32e-01 8.86e+01
        pdb=" NE  ARG B 147 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 147 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 147 "   -0.070 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 147 "    0.039 2.00e-02 2.50e+03
        pdb="HH11 ARG B 147 "    0.081 2.00e-02 2.50e+03
        pdb="HH12 ARG B 147 "    0.033 2.00e-02 2.50e+03
        pdb="HH21 ARG B 147 "    0.078 2.00e-02 2.50e+03
        pdb="HH22 ARG B 147 "   -0.090 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 147 "   -0.349 9.50e-02 1.11e+02   1.28e-01 7.83e+01
        pdb=" NE  ARG A 147 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 147 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 147 "   -0.062 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 147 "    0.039 2.00e-02 2.50e+03
        pdb="HH11 ARG A 147 "    0.066 2.00e-02 2.50e+03
        pdb="HH12 ARG A 147 "    0.038 2.00e-02 2.50e+03
        pdb="HH21 ARG A 147 "    0.072 2.00e-02 2.50e+03
        pdb="HH22 ARG A 147 "   -0.091 2.00e-02 2.50e+03
  ... (remaining 2005 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 661
        2.22 -     2.82: 24748
        2.82 -     3.41: 36293
        3.41 -     4.01: 47122
        4.01 -     4.60: 69085
  Nonbonded interactions: 177909
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 202 "
            pdb=" HG1 THR B 407 "
     model   vdw
     1.630 2.450
  nonbonded pdb=" OE1 GLU A 202 "
            pdb=" HG1 THR A 407 "
     model   vdw
     1.645 2.450
  nonbonded pdb=" HG  SER B  86 "
            pdb=" O   GLY B 141 "
     model   vdw
     1.704 2.450
  nonbonded pdb=" HG  SER A  86 "
            pdb=" O   GLY A 141 "
     model   vdw
     1.715 2.450
  nonbonded pdb=" O   VAL A 412 "
            pdb=" HG1 THR A 416 "
     model   vdw
     1.715 2.450
  ... (remaining 177904 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.920
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
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      :  0.013   0.036   6810  Z= 0.830
  Angle     :  1.796   7.292   9242  Z= 1.253
  Chirality :  0.090   0.409   1086
  Planarity :  0.012   0.104   1160
  Dihedral  : 10.815  83.495   2404
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.81 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.26 %
  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: -2.24 (0.25), residues: 884
  helix: -1.58 (0.16), residues: 656
  sheet:  None (None), residues: 0
  loop : -0.47 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 205 
 TYR   0.089   0.018   TYR A  75 
 PHE   0.047   0.009   PHE A 199 
 TRP   0.065   0.013   TRP B 125 
 HIS   0.009   0.003   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.01316 ( 6810)
  covalent geometry    : angle       1.79588 ( 9242)
  hydrogen bonds       : bond        0.29076 (  459)
  hydrogen bonds       : angle       7.71060 ( 1359)

*********************** 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
  103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7643 (tpt170)
REVERT: A  172 GLU cc_start: 0.8664 (pm20) cc_final: 0.8295 (tm-30)
REVERT: A  228 MET cc_start: 0.8767 (mmp) cc_final: 0.8225 (mmt)
REVERT: A  373 MET cc_start: 0.8447 (mtt) cc_final: 0.8212 (mtp)
REVERT: B  164 ASP cc_start: 0.8290 (m-30) cc_final: 0.7818 (m-30)
REVERT: B  172 GLU cc_start: 0.8458 (pm20) cc_final: 0.8140 (tm-30)
REVERT: B  373 MET cc_start: 0.8457 (mtt) cc_final: 0.8240 (mtp)
REVERT: B  425 MET cc_start: 0.8469 (mtt) cc_final: 0.8211 (mtm)
REVERT: B  433 THR cc_start: 0.8721 (m) cc_final: 0.8500 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2119
  time to fit residues: 28.8033
Evaluate side-chains
  84 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
B 327 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.119119 restraints weight = 22508.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.65
r_work: 0.3187 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6810  Z= 0.192
  Angle     :  0.638   5.352   9242  Z= 0.362
  Chirality :  0.042   0.146   1086
  Planarity :  0.006   0.035   1160
  Dihedral  :  5.068  23.997    946
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 0.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  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:  0.20 (0.28), residues: 884
  helix:  0.69 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.31 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 174 
 TYR   0.015   0.002   TYR B  75 
 PHE   0.022   0.002   PHE A  92 
 TRP   0.012   0.002   TRP B 253 
 HIS   0.006   0.002   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6810)
  covalent geometry    : angle       0.63819 ( 9242)
  hydrogen bonds       : bond        0.09452 (  459)
  hydrogen bonds       : angle       4.99448 ( 1359)

*********************** 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
  81 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.7534 (mmt) cc_final: 0.6849 (mmt)
REVERT: A  167 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7349 (mtt180)
REVERT: A  172 GLU cc_start: 0.7425 (pm20) cc_final: 0.6870 (tt0)
REVERT: A  228 MET cc_start: 0.8693 (mmp) cc_final: 0.8354 (mmm)
REVERT: A  290 LYS cc_start: 0.7200 (mttt) cc_final: 0.6959 (mttp)
REVERT: A  373 MET cc_start: 0.8336 (mtt) cc_final: 0.8061 (mtp)
REVERT: B  172 GLU cc_start: 0.7335 (pm20) cc_final: 0.6848 (tt0)
REVERT: B  228 MET cc_start: 0.8778 (mmt) cc_final: 0.8465 (mmm)
REVERT: B  373 MET cc_start: 0.8253 (mtt) cc_final: 0.8041 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2045
  time to fit residues: 21.9623
Evaluate side-chains
  77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 29 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0970
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 21 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.154355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.124086 restraints weight = 22547.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.80
r_work: 0.3259 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6810  Z= 0.129
  Angle     :  0.496   4.457   9242  Z= 0.273
  Chirality :  0.038   0.108   1086
  Planarity :  0.005   0.038   1160
  Dihedral  :  4.364  18.772    946
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 0.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.18 %
    Favored  : 95.67 %
  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:  1.10 (0.29), residues: 884
  helix:  1.40 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.21 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 174 
 TYR   0.036   0.002   TYR A 419 
 PHE   0.008   0.001   PHE B  92 
 TRP   0.007   0.001   TRP A 253 
 HIS   0.003   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6810)
  covalent geometry    : angle       0.49574 ( 9242)
  hydrogen bonds       : bond        0.06479 (  459)
  hydrogen bonds       : angle       4.33662 ( 1359)

*********************** 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
  81 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7260 (tp30)
REVERT: A  167 ARG cc_start: 0.7302 (mtp180) cc_final: 0.6478 (tpt170)
REVERT: A  172 GLU cc_start: 0.7255 (pm20) cc_final: 0.6609 (tt0)
REVERT: A  228 MET cc_start: 0.8544 (mmp) cc_final: 0.8257 (mmt)
REVERT: A  373 MET cc_start: 0.8123 (mtt) cc_final: 0.7897 (mtp)
REVERT: B   27 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7307 (tp30)
REVERT: B  172 GLU cc_start: 0.7148 (pm20) cc_final: 0.6573 (tt0)
REVERT: B  228 MET cc_start: 0.8609 (mmt) cc_final: 0.8386 (mmt)
REVERT: B  419 TYR cc_start: 0.7517 (m-80) cc_final: 0.6510 (p90)
  outliers start: 1
  outliers final: 1
  residues processed: 81
  average time/residue: 0.2251
  time to fit residues: 23.6668
Evaluate side-chains
  71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.147583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.117031 restraints weight = 22755.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.80
r_work: 0.3171 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6810  Z= 0.179
  Angle     :  0.535   4.431   9242  Z= 0.294
  Chirality :  0.039   0.124   1086
  Planarity :  0.005   0.041   1160
  Dihedral  :  4.280  18.825    946
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 1.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.37 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.29), residues: 884
  helix:  1.30 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.47 (0.39), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 174 
 TYR   0.012   0.002   TYR B 419 
 PHE   0.018   0.002   PHE A  92 
 TRP   0.008   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6810)
  covalent geometry    : angle       0.53513 ( 9242)
  hydrogen bonds       : bond        0.07867 (  459)
  hydrogen bonds       : angle       4.37861 ( 1359)

*********************** 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
  64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7222 (pm20) cc_final: 0.6626 (tt0)
REVERT: A  228 MET cc_start: 0.8703 (mmp) cc_final: 0.8359 (mmm)
REVERT: A  373 MET cc_start: 0.8288 (mtt) cc_final: 0.8037 (mtp)
REVERT: B  172 GLU cc_start: 0.7285 (pm20) cc_final: 0.6618 (tt0)
REVERT: B  228 MET cc_start: 0.8757 (mmt) cc_final: 0.8428 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 64
  average time/residue: 0.1759
  time to fit residues: 15.5426
Evaluate side-chains
  64 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain B residue  136 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 55 optimal weight:    0.1980
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3537 r_free = 0.3537 target = 0.140854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.106912 restraints weight = 22476.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.06
r_work: 0.3016 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6810  Z= 0.146
  Angle     :  0.493   4.364   9242  Z= 0.270
  Chirality :  0.037   0.117   1086
  Planarity :  0.005   0.041   1160
  Dihedral  :  4.169  18.117    946
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.97 %
    Favored  : 93.58 %
  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:  1.05 (0.29), residues: 884
  helix:  1.42 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.46 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 174 
 TYR   0.018   0.002   TYR B 419 
 PHE   0.015   0.001   PHE A  92 
 TRP   0.005   0.001   TRP B 125 
 HIS   0.002   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6810)
  covalent geometry    : angle       0.49346 ( 9242)
  hydrogen bonds       : bond        0.07014 (  459)
  hydrogen bonds       : angle       4.21541 ( 1359)

*********************** 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
  66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7106 (tp30)
REVERT: A  172 GLU cc_start: 0.6993 (pm20) cc_final: 0.6327 (tt0)
REVERT: A  210 TYR cc_start: 0.7823 (t80) cc_final: 0.7468 (t80)
REVERT: A  228 MET cc_start: 0.8548 (mmp) cc_final: 0.8204 (mmm)
REVERT: A  373 MET cc_start: 0.8046 (mtt) cc_final: 0.7775 (mtp)
REVERT: B  172 GLU cc_start: 0.7062 (pm20) cc_final: 0.6351 (tt0)
REVERT: B  228 MET cc_start: 0.8566 (mmt) cc_final: 0.8222 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 66
  average time/residue: 0.1843
  time to fit residues: 16.6753
Evaluate side-chains
  65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain B residue  136 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.154510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.123715 restraints weight = 22530.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.83
r_work: 0.3286 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6810  Z= 0.136
  Angle     :  0.478   4.369   9242  Z= 0.259
  Chirality :  0.037   0.116   1086
  Planarity :  0.005   0.041   1160
  Dihedral  :  4.026  16.761    946
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  5.97 %
    Favored  : 93.43 %
  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:  1.21 (0.29), residues: 884
  helix:  1.56 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.55 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 174 
 TYR   0.014   0.001   TYR A 419 
 PHE   0.014   0.001   PHE A  92 
 TRP   0.005   0.001   TRP A 125 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6810)
  covalent geometry    : angle       0.47753 ( 9242)
  hydrogen bonds       : bond        0.06561 (  459)
  hydrogen bonds       : angle       4.10645 ( 1359)

*********************** 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
  68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7105 (pm20) cc_final: 0.6479 (tt0)
REVERT: A  210 TYR cc_start: 0.7875 (t80) cc_final: 0.7565 (t80)
REVERT: A  228 MET cc_start: 0.8648 (mmp) cc_final: 0.8300 (mmm)
REVERT: A  373 MET cc_start: 0.8167 (mtt) cc_final: 0.7888 (mtp)
REVERT: B  172 GLU cc_start: 0.7160 (pm20) cc_final: 0.6499 (tt0)
REVERT: B  228 MET cc_start: 0.8691 (mmt) cc_final: 0.8356 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 67
  average time/residue: 0.1738
  time to fit residues: 15.9032
Evaluate side-chains
  66 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain B residue  136 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0030
   chunk 71 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.157473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.126904 restraints weight = 22185.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.82
r_work: 0.3296 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6810  Z= 0.107
  Angle     :  0.444   4.377   9242  Z= 0.239
  Chirality :  0.036   0.107   1086
  Planarity :  0.005   0.038   1160
  Dihedral  :  3.841  15.943    946
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  6.72 %
    Favored  : 92.84 %
  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:  1.63 (0.30), residues: 884
  helix:  1.89 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.51 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 174 
 TYR   0.019   0.001   TYR A 419 
 PHE   0.010   0.001   PHE A  92 
 TRP   0.005   0.001   TRP A 125 
 HIS   0.002   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 6810)
  covalent geometry    : angle       0.44408 ( 9242)
  hydrogen bonds       : bond        0.05555 (  459)
  hydrogen bonds       : angle       3.94061 ( 1359)

*********************** 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
  69 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7040 (pm20) cc_final: 0.6373 (tt0)
REVERT: A  210 TYR cc_start: 0.7832 (t80) cc_final: 0.7589 (t80)
REVERT: A  228 MET cc_start: 0.8642 (mmp) cc_final: 0.8244 (mmt)
REVERT: A  373 MET cc_start: 0.8077 (mtt) cc_final: 0.7871 (mtp)
REVERT: B  172 GLU cc_start: 0.7163 (pm20) cc_final: 0.6486 (tt0)
REVERT: B  228 MET cc_start: 0.8648 (mmt) cc_final: 0.8300 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 0.1703
  time to fit residues: 15.7602
Evaluate side-chains
  68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  136 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 36 optimal weight:    0.0040
   chunk 11 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.4792

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.159956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.129301 restraints weight = 22148.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.82
r_work: 0.3310 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6810  Z= 0.099
  Angle     :  0.431   5.296   9242  Z= 0.228
  Chirality :  0.036   0.110   1086
  Planarity :  0.005   0.039   1160
  Dihedral  :  3.651  15.893    946
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  6.87 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.30), residues: 884
  helix:  2.29 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.54 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.026   0.001   TYR A 419 
 PHE   0.008   0.001   PHE B  92 
 TRP   0.005   0.001   TRP A 125 
 HIS   0.002   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 6810)
  covalent geometry    : angle       0.43114 ( 9242)
  hydrogen bonds       : bond        0.04910 (  459)
  hydrogen bonds       : angle       3.78479 ( 1359)

*********************** 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
  68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  210 TYR cc_start: 0.7825 (t80) cc_final: 0.7617 (t80)
REVERT: A  228 MET cc_start: 0.8642 (mmp) cc_final: 0.8272 (mmt)
REVERT: B  172 GLU cc_start: 0.7255 (pm20) cc_final: 0.6604 (tt0)
REVERT: B  228 MET cc_start: 0.8669 (mmt) cc_final: 0.8294 (mmt)
REVERT: B  419 TYR cc_start: 0.8346 (m-80) cc_final: 0.6839 (p90)
  outliers start: 4
  outliers final: 4
  residues processed: 66
  average time/residue: 0.2028
  time to fit residues: 17.8611
Evaluate side-chains
  65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0980
   chunk 67 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.157964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.127683 restraints weight = 22286.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.79
r_work: 0.3303 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6810  Z= 0.110
  Angle     :  0.441   5.164   9242  Z= 0.233
  Chirality :  0.036   0.110   1086
  Planarity :  0.005   0.037   1160
  Dihedral  :  3.632  15.854    946
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 1.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  6.87 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.30), residues: 884
  helix:  2.27 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.54 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 174 
 TYR   0.012   0.001   TYR B 419 
 PHE   0.010   0.001   PHE A  92 
 TRP   0.004   0.001   TRP A 124 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6810)
  covalent geometry    : angle       0.44073 ( 9242)
  hydrogen bonds       : bond        0.05335 (  459)
  hydrogen bonds       : angle       3.80952 ( 1359)

*********************** 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
  68 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7108 (pm20) cc_final: 0.6457 (tt0)
REVERT: A  210 TYR cc_start: 0.7781 (t80) cc_final: 0.7577 (t80)
REVERT: A  228 MET cc_start: 0.8640 (mmp) cc_final: 0.8095 (mmp)
REVERT: B  172 GLU cc_start: 0.7258 (pm20) cc_final: 0.6543 (tt0)
REVERT: B  228 MET cc_start: 0.8678 (mmt) cc_final: 0.8335 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 67
  average time/residue: 0.1774
  time to fit residues: 16.3505
Evaluate side-chains
  67 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  201 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.3980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.151529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120428 restraints weight = 22248.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.83
r_work: 0.3209 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6810  Z= 0.103
  Angle     :  0.431   5.288   9242  Z= 0.228
  Chirality :  0.036   0.109   1086
  Planarity :  0.005   0.038   1160
  Dihedral  :  3.589  15.616    946
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 0.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  7.01 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.30), residues: 884
  helix:  2.38 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.42 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 174 
 TYR   0.010   0.001   TYR B 419 
 PHE   0.009   0.001   PHE A  92 
 TRP   0.004   0.001   TRP A 125 
 HIS   0.001   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 6810)
  covalent geometry    : angle       0.43115 ( 9242)
  hydrogen bonds       : bond        0.05078 (  459)
  hydrogen bonds       : angle       3.75625 ( 1359)

********************** 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 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 TYR cc_start: 0.7799 (t80) cc_final: 0.7586 (t80)
REVERT: A  228 MET cc_start: 0.8566 (mmp) cc_final: 0.8153 (mmt)
REVERT: B  172 GLU cc_start: 0.7248 (pm20) cc_final: 0.6576 (tt0)
REVERT: B  228 MET cc_start: 0.8601 (mmt) cc_final: 0.8274 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1834
  time to fit residues: 16.0816
Evaluate side-chains
  65 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  136 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0070
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.150467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.119275 restraints weight = 22408.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.84
r_work: 0.3194 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6810  Z= 0.110
  Angle     :  0.442   5.308   9242  Z= 0.233
  Chirality :  0.036   0.110   1086
  Planarity :  0.005   0.038   1160
  Dihedral  :  3.597  15.500    946
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 0.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  7.01 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.30), residues: 884
  helix:  2.31 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.45 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 174 
 TYR   0.015   0.001   TYR B 419 
 PHE   0.011   0.001   PHE A  92 
 TRP   0.004   0.001   TRP A 124 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6810)
  covalent geometry    : angle       0.44181 ( 9242)
  hydrogen bonds       : bond        0.05382 (  459)
  hydrogen bonds       : angle       3.78555 ( 1359)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3351.17 seconds
wall clock time: 57 minutes 25.00 seconds (3445.00 seconds total)