Starting phenix.real_space_refine
on Tue Mar 11 18:09:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ga3_29885/03_2025/8ga3_29885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ga3_29885/03_2025/8ga3_29885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ga3_29885/03_2025/8ga3_29885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ga3_29885/03_2025/8ga3_29885.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ga3_29885/03_2025/8ga3_29885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ga3_29885/03_2025/8ga3_29885.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.090
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     Cl      4      4.86       5
     C    4336      2.51       5
     N    1085      2.21       5
     O    1123      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6590
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3295
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3291
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    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: 4.30, per 1000 atoms: 0.65
  Number of scatterers: 6590
  At special positions: 0
  Unit cell: (73.425, 89.925, 110.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      4     17.00
     S      42     16.00
     O    1123      8.00
     N    1085      7.00
     C    4336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS B 249 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 249 " - pdb=" SG  CYS B 230 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 947.8 milliseconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 0 sheets defined
      72.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 28
      removed outlier: 3.655A  pdb=" N   ARG A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLN A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A  26 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 49
      removed outlier: 3.814A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLY A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 58
    Processing helix  chain 'A' and resid 60 through 64
      removed outlier: 3.733A  pdb=" N   ARG A  64 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 4.019A  pdb=" N   THR A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 102 through 105
      removed outlier: 3.615A  pdb=" N   GLY A 105 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 102 through 105'
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 3.596A  pdb=" N   LEU A 128 " --> pdb=" O   TRP A 124 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
      removed outlier: 3.564A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 166
      removed outlier: 3.888A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 190
      removed outlier: 3.677A  pdb=" N   ALA A 179 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 202
      removed outlier: 3.899A  pdb=" N   ILE A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.570A  pdb=" N   SER A 225 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TYR A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 280
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 280 through 285
      removed outlier: 4.065A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.752A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.654A  pdb=" N   LEU A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 326
      removed outlier: 3.532A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 4.708A  pdb=" N   ARG A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 358 through 363
    Processing helix  chain 'A' and resid 363 through 379
      removed outlier: 3.647A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 401
      removed outlier: 3.590A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 417
    Processing helix  chain 'A' and resid 422 through 439
      removed outlier: 3.516A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 457
      removed outlier: 3.706A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 67
      removed outlier: 3.559A  pdb=" N   PHE B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TRP B  59 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   MET B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA B  67 " --> pdb=" O   GLN B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 99
      removed outlier: 4.236A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 117
      removed outlier: 4.223A  pdb=" N   ALA B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
      Proline residue:  B 129  - end of helix
      removed outlier: 3.667A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 139
    Processing helix  chain 'B' and resid 140 through 142
      No H-bonds generated for 'chain 'B' and resid 140 through 142'
    Processing helix  chain 'B' and resid 148 through 166
      removed outlier: 3.591A  pdb=" N   VAL B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 188
      removed outlier: 3.629A  pdb=" N   LEU B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA B 182 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.775A  pdb=" N   ILE B 197 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 231
      removed outlier: 3.575A  pdb=" N   PHE B 219 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 280
      Proline residue:  B 267  - end of helix
      removed outlier: 3.866A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 309
      removed outlier: 3.873A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 324
      removed outlier: 3.587A  pdb=" N   THR B 324 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 346
      removed outlier: 3.516A  pdb=" N   PHE B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 351
      removed outlier: 3.528A  pdb=" N   SER B 350 " --> pdb=" O   CYS B 347 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY B 351 " --> pdb=" O   PHE B 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 347 through 351'
    Processing helix  chain 'B' and resid 357 through 362
    Processing helix  chain 'B' and resid 363 through 373
      removed outlier: 3.661A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 383
      removed outlier: 3.707A  pdb=" N   TYR B 382 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 379 through 383'
    Processing helix  chain 'B' and resid 387 through 395
      removed outlier: 4.002A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 401
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 418 through 422
    Processing helix  chain 'B' and resid 423 through 440
      removed outlier: 3.679A  pdb=" N   ALA B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 461
      removed outlier: 3.776A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 454 " --> pdb=" O   ALA B 450 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU B 461 " --> pdb=" O   GLU B 457 " (cutoff:3.500A)

    336 hydrogen bonds defined for protein.
    999 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.74

  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:
        1.22 -     1.34: 2062
        1.34 -     1.46: 1227
        1.46 -     1.57: 3365
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 6730
  Sorted by residual:
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.336  1.385 -0.049 1.23e-02 6.61e+03 1.59e+01
  bond pdb=" CA  ILE B 109 "
       pdb=" C   ILE B 109 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 8.80e-03 1.29e+04 2.26e+00
  bond pdb=" C   ILE A 109 "
       pdb=" N   PRO A 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.25e-02 6.40e+03 2.01e+00
  bond pdb=" C   LEU B 423 "
       pdb=" N   PRO B 424 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.017 1.25e-02 6.40e+03 1.81e+00
  bond pdb=" C   ARG B 205 "
       pdb=" N   PRO B 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 9.40e-03 1.13e+04 1.74e+00
  ... (remaining 6725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8799
        2.00 -     4.00: 278
        4.00 -     6.00: 41
        6.00 -     8.00: 24
        8.00 -    10.00: 5
  Bond angle restraints: 9147
  Sorted by residual:
  angle pdb=" N   LEU B 411 "
        pdb=" CA  LEU B 411 "
        pdb=" C   LEU B 411 "
      ideal   model   delta    sigma   weight residual
     114.62  108.19    6.43 1.14e+00 7.69e-01 3.18e+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  123.85   -3.52 8.00e-01 1.56e+00 1.94e+01
  angle pdb=" CA  ILE B 320 "
        pdb=" C   ILE B 320 "
        pdb=" N   PRO B 321 "
      ideal   model   delta    sigma   weight residual
     120.83  123.41   -2.58 6.10e-01 2.69e+00 1.79e+01
  angle pdb=" C   GLY B 108 "
        pdb=" N   ILE B 109 "
        pdb=" CA  ILE B 109 "
      ideal   model   delta    sigma   weight residual
     120.24  122.73   -2.49 6.30e-01 2.52e+00 1.57e+01
  angle pdb=" C   THR B 211 "
        pdb=" N   LEU B 212 "
        pdb=" CA  LEU B 212 "
      ideal   model   delta    sigma   weight residual
     121.54  129.01   -7.47 1.91e+00 2.74e-01 1.53e+01
  ... (remaining 9142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3426
       17.85 -    35.70: 395
       35.70 -    53.55: 59
       53.55 -    71.40: 10
       71.40 -    89.24: 3
  Dihedral angle restraints: 3893
    sinusoidal: 1447
      harmonic: 2446
  Sorted by residual:
  dihedral pdb=" CB  CYS A 230 "
           pdb=" SG  CYS A 230 "
           pdb=" SG  CYS B 249 "
           pdb=" CB  CYS B 249 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.98  -60.98     1      1.00e+01 1.00e-02 4.94e+01
  dihedral pdb=" CA  CYS A 249 "
           pdb=" C   CYS A 249 "
           pdb=" N   ASN A 250 "
           pdb=" CA  ASN A 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.86   27.14     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  ASP A 118 "
           pdb=" C   ASP A 118 "
           pdb=" N   GLN A 119 "
           pdb=" CA  GLN A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.25  -26.75     0      5.00e+00 4.00e-02 2.86e+01
  ... (remaining 3890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 891
       0.063 -    0.125: 169
       0.125 -    0.188: 18
       0.188 -    0.250: 4
       0.250 -    0.313: 2
  Chirality restraints: 1084
  Sorted by residual:
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CB  THR B  31 "
            pdb=" CA  THR B  31 "
            pdb=" OG1 THR B  31 "
            pdb=" CG2 THR B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  THR B  31 "
            pdb=" N   THR B  31 "
            pdb=" C   THR B  31 "
            pdb=" CB  THR B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1081 not shown)

  Planarity restraints: 1147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "    0.045 5.00e-02 4.00e+02   6.66e-02 7.09e+00
        pdb=" N   PRO B 359 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 266 "    0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO A 267 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 423 "   -0.043 5.00e-02 4.00e+02   6.41e-02 6.56e+00
        pdb=" N   PRO A 424 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 424 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 424 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1144 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2042
        2.81 -     3.34: 5683
        3.34 -     3.86: 11120
        3.86 -     4.38: 13691
        4.38 -     4.90: 22872
  Nonbonded interactions: 55408
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ARG A 147 "
            pdb=" OG1 THR A 151 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   LEU B 435 "
            pdb=" OG1 THR B 439 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLY B 141 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   LEU A 345 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.327 3.040
  ... (remaining 55403 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 19 through 20 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 21 through 461 or resid 501 through 502))
  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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.440
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
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      :  0.005   0.052   6730  Z= 0.307
  Angle     :  0.888   9.996   9147  Z= 0.471
  Chirality :  0.051   0.313   1084
  Planarity :  0.007   0.067   1147
  Dihedral  : 14.759  89.245   2343
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.60 (0.16), residues: 882
  helix: -4.64 (0.08), residues: 604
  sheet:  None (None), residues: 0
  loop : -3.13 (0.29), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP B 291 
 HIS   0.007   0.002   HIS B 284 
 PHE   0.009   0.001   PHE A 219 
 TYR   0.019   0.002   TYR A 210 
 ARG   0.003   0.000   ARG A  64 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8663 (m-30) cc_final: 0.8459 (m-30)
REVERT: A  174 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6544 (mtp180)
REVERT: B  290 LYS cc_start: 0.7985 (mttp) cc_final: 0.7784 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.2276
  time to fit residues: 28.7875
Evaluate side-chains
  74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0000
   chunk 44 optimal weight:    0.0060
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.5200

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

Flipped N/Q/H residues before XYZ refinement:
B  70 HIS
B 157 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.165362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.138181 restraints weight = 7276.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.88
r_work: 0.3413 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6730  Z= 0.191
  Angle     :  0.615   6.360   9147  Z= 0.312
  Chirality :  0.042   0.149   1084
  Planarity :  0.006   0.046   1147
  Dihedral  :  5.457  24.884    934
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.08 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.51 (0.22), residues: 882
  helix: -2.81 (0.16), residues: 630
  sheet:  None (None), residues: 0
  loop : -2.91 (0.32), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.007   0.001   PHE A 219 
 TYR   0.009   0.001   TYR A 210 
 ARG   0.003   0.000   ARG B 167 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.604 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.6976 (mtt90)
REVERT: A  147 ARG cc_start: 0.7832 (ptt-90) cc_final: 0.7451 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6773 (mtt180) cc_final: 0.5937 (mtp180)
REVERT: A  186 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: A  294 MET cc_start: 0.7127 (ttp) cc_final: 0.6598 (ttt)
  outliers start: 9
  outliers final: 2
  residues processed: 79
  average time/residue: 0.1844
  time to fit residues: 19.7677
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0070
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.170414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.145026 restraints weight = 7231.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.77
r_work: 0.3393 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6730  Z= 0.191
  Angle     :  0.582   7.325   9147  Z= 0.289
  Chirality :  0.042   0.129   1084
  Planarity :  0.004   0.044   1147
  Dihedral  :  5.169  24.423    934
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.59 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.26), residues: 882
  helix: -1.69 (0.19), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.71 (0.33), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.007   0.001   PHE A 379 
 TYR   0.008   0.001   TYR B  94 
 ARG   0.002   0.000   ARG B 167 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.6926 (mtt90)
REVERT: A  174 ARG cc_start: 0.6759 (mtt180) cc_final: 0.5910 (mtp180)
REVERT: A  294 MET cc_start: 0.7236 (ttp) cc_final: 0.6752 (ttt)
REVERT: B   91 MET cc_start: 0.7629 (mtp) cc_final: 0.7421 (mtt)
REVERT: B  198 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7427 (mp)
  outliers start: 12
  outliers final: 4
  residues processed: 77
  average time/residue: 0.1910
  time to fit residues: 20.0274
Evaluate side-chains
  69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  198 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 87 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 86 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.169591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.144166 restraints weight = 7205.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.78
r_work: 0.3380 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6730  Z= 0.206
  Angle     :  0.575   7.808   9147  Z= 0.284
  Chirality :  0.042   0.153   1084
  Planarity :  0.004   0.046   1147
  Dihedral  :  5.086  24.047    934
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.42 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.27), residues: 882
  helix: -1.14 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.68 (0.33), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 291 
 HIS   0.003   0.001   HIS B 284 
 PHE   0.006   0.001   PHE B 307 
 TYR   0.007   0.001   TYR B  94 
 ARG   0.005   0.000   ARG A 147 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7763 (mtt-85) cc_final: 0.6966 (mtt90)
REVERT: A  174 ARG cc_start: 0.6775 (mtt180) cc_final: 0.5905 (mtp180)
REVERT: A  294 MET cc_start: 0.7263 (ttp) cc_final: 0.6724 (ttp)
REVERT: B   65 MET cc_start: 0.7507 (mmt) cc_final: 0.7054 (mmm)
REVERT: B   91 MET cc_start: 0.7631 (mtp) cc_final: 0.7420 (mtt)
REVERT: B  198 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7392 (mp)
  outliers start: 12
  outliers final: 6
  residues processed: 76
  average time/residue: 0.1911
  time to fit residues: 20.2375
Evaluate side-chains
  69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  198 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 35 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0670
   chunk 61 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0980
   chunk 83 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.166356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.139134 restraints weight = 7251.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.87
r_work: 0.3498 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   6730  Z= 0.171
  Angle     :  0.585  14.181   9147  Z= 0.287
  Chirality :  0.042   0.149   1084
  Planarity :  0.004   0.045   1147
  Dihedral  :  5.043  27.306    934
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.72 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.28), residues: 882
  helix: -0.80 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.63 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.019   0.001   PHE B  95 
 TYR   0.009   0.001   TYR A 229 
 ARG   0.004   0.000   ARG A 147 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.6925 (mtt90)
REVERT: A  174 ARG cc_start: 0.6753 (mtt180) cc_final: 0.5876 (mtp180)
REVERT: A  294 MET cc_start: 0.7250 (ttp) cc_final: 0.6756 (ttt)
REVERT: B   65 MET cc_start: 0.7464 (mmt) cc_final: 0.7005 (mmm)
REVERT: B  198 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7341 (mp)
  outliers start: 13
  outliers final: 7
  residues processed: 77
  average time/residue: 0.2124
  time to fit residues: 22.0743
Evaluate side-chains
  70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0000
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.4584

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN
B 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.166397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.138816 restraints weight = 7210.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.88
r_work: 0.3401 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6730  Z= 0.174
  Angle     :  0.565  11.706   9147  Z= 0.279
  Chirality :  0.041   0.140   1084
  Planarity :  0.004   0.046   1147
  Dihedral  :  4.910  24.673    934
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.48 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.28), residues: 882
  helix: -0.55 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.62 (0.33), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.020   0.001   PHE B  95 
 TYR   0.008   0.001   TYR A 229 
 ARG   0.003   0.000   ARG A 147 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7722 (mtt-85) cc_final: 0.7100 (mtm-85)
REVERT: A  174 ARG cc_start: 0.6784 (mtt180) cc_final: 0.5916 (mtp180)
REVERT: A  294 MET cc_start: 0.7226 (ttp) cc_final: 0.6725 (ttt)
REVERT: B   65 MET cc_start: 0.7489 (mmt) cc_final: 0.7056 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.1871
  time to fit residues: 17.8979
Evaluate side-chains
  65 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0050
   chunk 73 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0070
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.3612

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.167647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.140105 restraints weight = 7185.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.88
r_work: 0.3459 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   6730  Z= 0.160
  Angle     :  0.545   8.769   9147  Z= 0.269
  Chirality :  0.041   0.189   1084
  Planarity :  0.004   0.045   1147
  Dihedral  :  4.841  25.096    934
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.17 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.28), residues: 882
  helix: -0.27 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.61 (0.33), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 291 
 HIS   0.002   0.000   HIS A 383 
 PHE   0.020   0.001   PHE B  95 
 TYR   0.005   0.001   TYR A 229 
 ARG   0.003   0.000   ARG A 147 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7092 (mtm-85)
REVERT: A  147 ARG cc_start: 0.7716 (ptt-90) cc_final: 0.7484 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6789 (mtt180) cc_final: 0.5916 (mtp180)
REVERT: A  282 ARG cc_start: 0.7327 (mpt90) cc_final: 0.6859 (mtm110)
REVERT: A  294 MET cc_start: 0.7281 (ttp) cc_final: 0.6767 (ttt)
REVERT: B   65 MET cc_start: 0.7474 (mmt) cc_final: 0.7033 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 74
  average time/residue: 0.2124
  time to fit residues: 21.0596
Evaluate side-chains
  67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.166247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.138651 restraints weight = 7227.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.87
r_work: 0.3363 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6730  Z= 0.218
  Angle     :  0.585  10.664   9147  Z= 0.286
  Chirality :  0.043   0.181   1084
  Planarity :  0.004   0.046   1147
  Dihedral  :  4.926  24.454    934
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.08 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.28), residues: 882
  helix: -0.21 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.53 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.021   0.001   PHE B  95 
 TYR   0.007   0.001   TYR A 229 
 ARG   0.003   0.000   ARG A 147 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7099 (mtm-85)
REVERT: A  174 ARG cc_start: 0.6808 (mtt180) cc_final: 0.5923 (mtp180)
REVERT: A  282 ARG cc_start: 0.7391 (mpt90) cc_final: 0.6849 (mtm110)
REVERT: A  294 MET cc_start: 0.7202 (ttp) cc_final: 0.6694 (ttt)
REVERT: B   65 MET cc_start: 0.7498 (mmt) cc_final: 0.7064 (mmm)
  outliers start: 10
  outliers final: 8
  residues processed: 69
  average time/residue: 0.2224
  time to fit residues: 20.4765
Evaluate side-chains
  68 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   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 = 0.3870 r_free = 0.3870 target = 0.166653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.139153 restraints weight = 7256.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 1.87
r_work: 0.3371 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6730  Z= 0.196
  Angle     :  0.572   9.992   9147  Z= 0.280
  Chirality :  0.042   0.169   1084
  Planarity :  0.004   0.046   1147
  Dihedral  :  4.915  26.218    934
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.93 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.28), residues: 882
  helix: -0.08 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.52 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 
 PHE   0.022   0.001   PHE B  95 
 TYR   0.006   0.001   TYR B 229 
 ARG   0.006   0.000   ARG A 147 

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7716 (mtt-85) cc_final: 0.7109 (mtm-85)
REVERT: A  147 ARG cc_start: 0.7781 (ptt-90) cc_final: 0.7542 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6801 (mtt180) cc_final: 0.5915 (mtp180)
REVERT: A  282 ARG cc_start: 0.7388 (mpt90) cc_final: 0.6892 (mtm110)
REVERT: A  294 MET cc_start: 0.7199 (ttp) cc_final: 0.6684 (ttt)
REVERT: B   65 MET cc_start: 0.7482 (mmt) cc_final: 0.7060 (mmm)
  outliers start: 9
  outliers final: 9
  residues processed: 71
  average time/residue: 0.2335
  time to fit residues: 22.1757
Evaluate side-chains
  70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 62.91 > 50:
  distance: 120 - 124:  12.986
  distance: 124 - 125:   4.007
  distance: 125 - 126:  19.158
  distance: 125 - 128:   6.188
  distance: 126 - 127:  28.682
  distance: 126 - 135:   4.887
  distance: 128 - 129:   9.828
  distance: 129 - 130:  10.754
  distance: 129 - 131:  16.466
  distance: 130 - 132:  15.191
  distance: 131 - 133:  16.683
  distance: 132 - 134:  11.163
  distance: 133 - 134:  17.080
  distance: 135 - 136:  19.530
  distance: 136 - 137:  12.438
  distance: 136 - 139:  22.002
  distance: 137 - 138:   9.747
  distance: 137 - 141:  35.396
  distance: 139 - 140:  25.315
  distance: 141 - 142:  14.489
  distance: 142 - 143:  19.251
  distance: 142 - 145:   5.578
  distance: 143 - 144:  28.571
  distance: 143 - 147:  18.992
  distance: 145 - 146:  20.628
  distance: 147 - 148:  36.327
  distance: 148 - 149:  20.233
  distance: 149 - 150:  57.554
  distance: 149 - 151:  29.119
  distance: 151 - 152:  27.662
  distance: 152 - 153:   9.842
  distance: 152 - 155:  54.427
  distance: 153 - 154:  19.348
  distance: 153 - 156:  37.585
  distance: 156 - 157:  11.512
  distance: 156 - 162:  18.759
  distance: 157 - 158:  23.441
  distance: 157 - 160:  32.298
  distance: 158 - 159:  35.760
  distance: 158 - 163:  17.168
  distance: 160 - 161:   5.506
  distance: 161 - 162:  23.156
  distance: 163 - 164:  22.406
  distance: 164 - 165:  28.381
  distance: 165 - 166:  54.626
  distance: 165 - 167:  18.971
  distance: 167 - 168:  31.852
  distance: 168 - 169:  25.819
  distance: 169 - 170:  21.105
  distance: 169 - 171:  12.577
  distance: 171 - 172:  11.184
  distance: 172 - 173:  17.781
  distance: 172 - 175:  24.073
  distance: 173 - 174:  24.173
  distance: 173 - 179:  21.504
  distance: 175 - 176:  17.354
  distance: 175 - 177:  19.303
  distance: 176 - 178:  35.939
  distance: 179 - 180:   7.775
  distance: 180 - 181:  11.455
  distance: 180 - 183:   7.112
  distance: 181 - 182:   8.716
  distance: 181 - 190:   7.488
  distance: 182 - 209:   8.620
  distance: 183 - 184:   7.843
  distance: 184 - 185:   6.302
  distance: 184 - 186:   7.675
  distance: 185 - 187:  21.557
  distance: 186 - 188:  16.499
  distance: 187 - 189:   8.441
  distance: 188 - 189:  13.413