Starting phenix.real_space_refine
on Sat Aug 23 10:14:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxg_40851/08_2025/8sxg_40851.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxg_40851/08_2025/8sxg_40851.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxg_40851/08_2025/8sxg_40851.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxg_40851/08_2025/8sxg_40851.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxg_40851/08_2025/8sxg_40851.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxg_40851/08_2025/8sxg_40851.cif"
  }
  resolution = 4.14
  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=   0.000 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    7109      2.51       5
     N    2021      2.21       5
     O    2225      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11372
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2748
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 20, 'TRANS': 345}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2723
          Classifications: {'peptide': 363}
          Link IDs: {'PTRANS': 20, 'TRANS': 342}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4248
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 512}
    Chain: "D"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 30
          Classifications: {'peptide': 6}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'TRANS': 5}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'UNK:plan-1': 6}
          Unresolved non-hydrogen planarities: 6
    Chain: "E"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1623
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 10, 'TRANS': 205}
          Chain breaks: 2
  Time building chain proxies: 1.95, per 1000 atoms: 0.17
  Number of scatterers: 11372
  At special positions: 0
  Unit cell: (91.908, 141.588, 142.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      17     16.00
     O    2225      8.00
     N    2021      7.00
     C    7109      6.00
    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: 1.08
  Conformation dependent library (CDL) restraints added in 544.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2728

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 14 sheets defined
      55.5% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 60
      removed outlier: 3.902A  pdb=" N   LEU A  46 " --> pdb=" O   PRO A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 82
      removed outlier: 4.183A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 101
    Processing helix  chain 'A' and resid 129 through 133
    Processing helix  chain 'A' and resid 152 through 161
    Processing helix  chain 'A' and resid 214 through 230
    Processing helix  chain 'A' and resid 248 through 260
      removed outlier: 3.808A  pdb=" N   PHE A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 301 through 314
    Processing helix  chain 'A' and resid 412 through 417
      removed outlier: 3.885A  pdb=" N   SER A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 434
      removed outlier: 3.581A  pdb=" N   SER A 421 " --> pdb=" O   ASP A 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 60
      removed outlier: 3.873A  pdb=" N   LEU B  46 " --> pdb=" O   PRO B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 80
    Processing helix  chain 'B' and resid 89 through 98
      removed outlier: 3.851A  pdb=" N   GLU B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 132
    Processing helix  chain 'B' and resid 152 through 161
    Processing helix  chain 'B' and resid 214 through 230
      removed outlier: 3.631A  pdb=" N   GLU B 218 " --> pdb=" O   ASN B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 259
      removed outlier: 3.572A  pdb=" N   ALA B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 276
      removed outlier: 4.013A  pdb=" N   GLU B 276 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
    Processing helix  chain 'B' and resid 356 through 361
      removed outlier: 3.637A  pdb=" N   GLN B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 417
      removed outlier: 3.791A  pdb=" N   SER B 416 " --> pdb=" O   ARG B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 435
      removed outlier: 4.022A  pdb=" N   VAL B 432 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   THR B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 63
      removed outlier: 3.617A  pdb=" N   LEU C  57 " --> pdb=" O   LEU C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 83
      removed outlier: 3.741A  pdb=" N   ALA C  71 " --> pdb=" O   ARG C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 99
    Processing helix  chain 'C' and resid 101 through 115
    Processing helix  chain 'C' and resid 118 through 133
    Processing helix  chain 'C' and resid 136 through 146
    Processing helix  chain 'C' and resid 154 through 163
      removed outlier: 4.171A  pdb=" N   GLU C 163 " --> pdb=" O   LEU C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 183
    Processing helix  chain 'C' and resid 186 through 201
      removed outlier: 3.951A  pdb=" N   LEU C 190 " --> pdb=" O   ASN C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 213
      removed outlier: 4.295A  pdb=" N   ALA C 206 " --> pdb=" O   ARG C 202 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN C 213 " --> pdb=" O   LEU C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 219
      removed outlier: 4.075A  pdb=" N   ARG C 217 " --> pdb=" O   ASN C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 233
      removed outlier: 3.577A  pdb=" N   LEU C 223 " --> pdb=" O   GLU C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 250
      Proline residue:  C 241  - end of helix
    Processing helix  chain 'C' and resid 253 through 267
      removed outlier: 4.161A  pdb=" N   ARG C 257 " --> pdb=" O   ASP C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 284
    Processing helix  chain 'C' and resid 287 through 301
      removed outlier: 3.617A  pdb=" N   ARG C 291 " --> pdb=" O   ASP C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 318
    Processing helix  chain 'C' and resid 320 through 335
    Processing helix  chain 'C' and resid 338 through 348
      removed outlier: 3.958A  pdb=" N   VAL C 348 " --> pdb=" O   GLU C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 353 through 369
      removed outlier: 3.577A  pdb=" N   ALA C 357 " --> pdb=" O   ASP C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 385
    Processing helix  chain 'C' and resid 385 through 403
      removed outlier: 3.856A  pdb=" N   GLN C 391 " --> pdb=" O   ASP C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 420
    Processing helix  chain 'C' and resid 423 through 438
      removed outlier: 3.619A  pdb=" N   LEU C 427 " --> pdb=" O   ASP C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 454
    Processing helix  chain 'C' and resid 457 through 471
      removed outlier: 3.678A  pdb=" N   LEU C 461 " --> pdb=" O   ASN C 457 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 475 through 489
    Processing helix  chain 'C' and resid 492 through 507
    Processing helix  chain 'C' and resid 509 through 523
    Processing helix  chain 'C' and resid 525 through 540
    Processing helix  chain 'C' and resid 541 through 556
      removed outlier: 3.630A  pdb=" N   ALA C 545 " --> pdb=" O   ARG C 541 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 571
    Processing helix  chain 'E' and resid 214 through 230
    Processing helix  chain 'E' and resid 248 through 260
      removed outlier: 3.682A  pdb=" N   PHE E 259 " --> pdb=" O   VAL E 255 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 302 through 314
    Processing helix  chain 'E' and resid 412 through 417
      removed outlier: 3.866A  pdb=" N   SER E 416 " --> pdb=" O   ARG E 412 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASP E 417 " --> pdb=" O   PRO E 413 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 412 through 417'
    Processing helix  chain 'E' and resid 417 through 433
      removed outlier: 3.558A  pdb=" N   SER E 421 " --> pdb=" O   ASP E 417 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 3.637A  pdb=" N   TYR A 267 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87
      removed outlier: 5.686A  pdb=" N   LYS A 343 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU A 334 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   THR A 345 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   THR A 332 " --> pdb=" O   THR A 345 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106
      removed outlier: 3.650A  pdb=" N   ALA A 187 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114
      removed outlier: 6.996A  pdb=" N   GLU A 110 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ASP A 138 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 114
      removed outlier: 6.996A  pdb=" N   GLU A 110 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ASP A 138 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   THR A 171 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ILE A 143 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   THR A 169 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 200
      removed outlier: 7.073A  pdb=" N   TYR A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ALA A 204 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   ASP A 240 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   LEU A 206 " --> pdb=" O   ASP A 240 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE A 296 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 375
    Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 114
      removed outlier: 7.021A  pdb=" N   GLU B 110 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LYS B 119 " --> pdb=" O   GLY B 112 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE B 118 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 114
      removed outlier: 7.021A  pdb=" N   GLU B 110 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LYS B 119 " --> pdb=" O   GLY B 112 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE B 118 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   THR B 171 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   ILE B 143 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   THR B 169 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE B 172 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200
      removed outlier: 6.688A  pdb=" N   TYR B 203 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 278
      removed outlier: 3.646A  pdb=" N   LEU B 277 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LYS B 269 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA B 347 " --> pdb=" O   VAL B 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 334 through 335
    Processing sheet with id=AB4, first strand: chain 'E' and resid 197 through 200
      removed outlier: 5.556A  pdb=" N   VAL E 198 " --> pdb=" O   TYR E 205 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   TYR E 205 " --> pdb=" O   VAL E 198 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   ALA E 204 " --> pdb=" O   VAL E 238 " (cutoff:3.500A)
      removed outlier: 8.298A  pdb=" N   ASP E 240 " --> pdb=" O   ALA E 204 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU E 206 " --> pdb=" O   ASP E 240 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU E 237 " --> pdb=" O   VAL E 293 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 264 through 266

    647 hydrogen bonds defined for protein.
    1872 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: 1.94

  Time building geometry restraints manager: 1.33 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: 3954
        1.34 -     1.46: 1228
        1.46 -     1.57: 6320
        1.57 -     1.69: 0
        1.69 -     1.81: 33
  Bond restraints: 11535
  Sorted by residual:
  bond pdb=" CG  GLU C 344 "
       pdb=" CD  GLU C 344 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 1.01e+00
  bond pdb=" N   SER B 193 "
       pdb=" CA  SER B 193 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.29e-02 6.01e+03 6.02e-01
  bond pdb=" C   GLU A 200 "
       pdb=" N   PRO A 201 "
    ideal  model  delta    sigma   weight residual
    1.332  1.340 -0.008 1.12e-02 7.97e+03 5.73e-01
  bond pdb=" N   VAL B 290 "
       pdb=" CA  VAL B 290 "
    ideal  model  delta    sigma   weight residual
    1.468  1.460  0.008 1.05e-02 9.07e+03 5.69e-01
  bond pdb=" N   ALA B 302 "
       pdb=" CA  ALA B 302 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.29e-02 6.01e+03 4.92e-01
  ... (remaining 11530 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 14991
        1.07 -     2.14: 466
        2.14 -     3.21: 94
        3.21 -     4.28: 48
        4.28 -     5.35: 5
  Bond angle restraints: 15604
  Sorted by residual:
  angle pdb=" N   ARG E 434 "
        pdb=" CA  ARG E 434 "
        pdb=" CB  ARG E 434 "
      ideal   model   delta    sigma   weight residual
     114.17  110.82    3.35 1.14e+00 7.69e-01 8.65e+00
  angle pdb=" N   GLU C 344 "
        pdb=" CA  GLU C 344 "
        pdb=" CB  GLU C 344 "
      ideal   model   delta    sigma   weight residual
     110.22  114.27   -4.05 1.54e+00 4.22e-01 6.92e+00
  angle pdb=" C   ALA B 302 "
        pdb=" CA  ALA B 302 "
        pdb=" CB  ALA B 302 "
      ideal   model   delta    sigma   weight residual
     110.42  115.65   -5.23 1.99e+00 2.53e-01 6.91e+00
  angle pdb=" C   SER B 193 "
        pdb=" CA  SER B 193 "
        pdb=" CB  SER B 193 "
      ideal   model   delta    sigma   weight residual
     110.42  115.60   -5.18 1.99e+00 2.53e-01 6.78e+00
  angle pdb=" C   LEU B 311 "
        pdb=" N   GLN B 312 "
        pdb=" CA  GLN B 312 "
      ideal   model   delta    sigma   weight residual
     121.64  116.29    5.35 2.13e+00 2.20e-01 6.30e+00
  ... (remaining 15599 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 6422
       17.94 -    35.88: 568
       35.88 -    53.82: 90
       53.82 -    71.76: 13
       71.76 -    89.70: 13
  Dihedral angle restraints: 7106
    sinusoidal: 2862
      harmonic: 4244
  Sorted by residual:
  dihedral pdb=" CA  ASP A 313 "
           pdb=" C   ASP A 313 "
           pdb=" N   GLN A 314 "
           pdb=" CA  GLN A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ASN E 230 "
           pdb=" C   ASN E 230 "
           pdb=" N   LYS E 231 "
           pdb=" CA  LYS E 231 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  ALA A  58 "
           pdb=" C   ALA A  58 "
           pdb=" N   ALA A  59 "
           pdb=" CA  ALA A  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.70  -16.30     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 7103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1175
       0.028 -    0.056: 380
       0.056 -    0.084: 104
       0.084 -    0.112: 78
       0.112 -    0.140: 34
  Chirality restraints: 1771
  Sorted by residual:
  chirality pdb=" CA  ILE A 208 "
            pdb=" N   ILE A 208 "
            pdb=" C   ILE A 208 "
            pdb=" CB  ILE A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.88e-01
  chirality pdb=" CA  ILE B 168 "
            pdb=" N   ILE B 168 "
            pdb=" C   ILE B 168 "
            pdb=" CB  ILE B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE A 143 "
            pdb=" N   ILE A 143 "
            pdb=" C   ILE A 143 "
            pdb=" CB  ILE A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 1768 not shown)

  Planarity restraints: 2081
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  89 "    0.033 5.00e-02 4.00e+02   5.04e-02 4.07e+00
        pdb=" N   PRO A  90 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A  90 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  90 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 415 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.00e+00
        pdb=" C   GLU C 415 "    0.024 2.00e-02 2.50e+03
        pdb=" O   GLU C 415 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY C 416 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  57 "   -0.007 2.00e-02 2.50e+03   1.37e-02 1.88e+00
        pdb=" C   LEU C  57 "    0.024 2.00e-02 2.50e+03
        pdb=" O   LEU C  57 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL C  58 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2078 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 110
        2.49 -     3.09: 9088
        3.09 -     3.70: 18427
        3.70 -     4.30: 25336
        4.30 -     4.90: 41450
  Nonbonded interactions: 94411
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 193 "
            pdb=" OE1 GLU B 218 "
     model   vdw
     1.889 3.040
  nonbonded pdb=" O   ASN E 297 "
            pdb=" OG1 THR E 322 "
     model   vdw
     2.038 3.040
  nonbonded pdb=" O   SER B 193 "
            pdb=" OG1 THR B 209 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" NH1 ARG B 207 "
            pdb=" O   ILE B 208 "
     model   vdw
     2.073 3.120
  nonbonded pdb=" O   VAL E 248 "
            pdb=" OG  SER E 251 "
     model   vdw
     2.091 3.040
  ... (remaining 94406 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 38 through 373 or resid 410 through 436))
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.520
  Find NCS groups from input model:        0.090
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
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      :  0.002   0.026  11535  Z= 0.106
  Angle     :  0.499   5.347  15604  Z= 0.263
  Chirality :  0.038   0.140   1771
  Planarity :  0.004   0.050   2081
  Dihedral  : 14.007  89.698   4378
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  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 aren not related in a simple way.
  whole:  0.78 (0.23), residues: 1461
  helix:  1.78 (0.20), residues: 745
  sheet: -0.96 (0.42), residues: 178
  loop : -0.72 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 340 
 TYR   0.012   0.001   TYR C  54 
 PHE   0.010   0.001   PHE C 326 
 TRP   0.004   0.001   TRP C 537 
 HIS   0.006   0.001   HIS C 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (11535)
  covalent geometry    : angle       0.49949 (15604)
  hydrogen bonds       : bond        0.16273 (  632)
  hydrogen bonds       : angle       6.50276 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1539 (tpp) cc_final: 0.1306 (tpp)
REVERT: E  265 ILE cc_start: 0.8830 (mm) cc_final: 0.8468 (mm)
REVERT: E  320 MET cc_start: 0.8992 (ttp) cc_final: 0.8589 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1115
  time to fit residues: 10.5883
Evaluate side-chains
  44 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 314 GLN
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 147 ASN
C 218 HIS
C 250 HIS
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 518 GLN
C 521 GLN
E 230 ASN
** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 396 ASN
E 422 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.088100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.070257 restraints weight = 56435.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068872 restraints weight = 71476.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.069345 restraints weight = 78129.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.069828 restraints weight = 50616.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.070157 restraints weight = 44446.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.088  11535  Z= 0.416
  Angle     :  0.877   9.694  15604  Z= 0.441
  Chirality :  0.048   0.163   1771
  Planarity :  0.006   0.051   2081
  Dihedral  :  5.542  27.094   1613
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  8.42 %
    Favored  : 91.08 %
  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 aren not related in a simple way.
  whole: -0.20 (0.22), residues: 1461
  helix:  0.81 (0.18), residues: 764
  sheet: -1.24 (0.44), residues: 155
  loop : -1.05 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 242 
 TYR   0.033   0.003   TYR B 205 
 PHE   0.026   0.003   PHE B 211 
 TRP   0.009   0.002   TRP C 537 
 HIS   0.007   0.002   HIS C 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00951 (11535)
  covalent geometry    : angle       0.87702 (15604)
  hydrogen bonds       : bond        0.05469 (  632)
  hydrogen bonds       : angle       5.72398 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  114 SER cc_start: 0.8526 (p) cc_final: 0.8190 (t)
REVERT: C  432 MET cc_start: 0.1623 (tpp) cc_final: 0.1366 (tpp)
  outliers start: 6
  outliers final: 2
  residues processed: 51
  average time/residue: 0.1049
  time to fit residues: 8.4551
Evaluate side-chains
  40 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 135 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 335 GLN
E 230 ASN
E 314 GLN
** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.092651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.074422 restraints weight = 56351.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.072745 restraints weight = 59652.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.073393 restraints weight = 58071.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.073763 restraints weight = 38279.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.073884 restraints weight = 37261.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11535  Z= 0.135
  Angle     :  0.578   7.310  15604  Z= 0.297
  Chirality :  0.041   0.141   1771
  Planarity :  0.004   0.038   2081
  Dihedral  :  4.704  22.223   1613
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  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 aren not related in a simple way.
  whole:  0.49 (0.22), residues: 1461
  helix:  1.42 (0.18), residues: 767
  sheet: -1.06 (0.43), residues: 162
  loop : -0.76 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 340 
 TYR   0.016   0.002   TYR B 205 
 PHE   0.009   0.001   PHE B 104 
 TRP   0.018   0.002   TRP C 537 
 HIS   0.004   0.001   HIS C 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11535)
  covalent geometry    : angle       0.57809 (15604)
  hydrogen bonds       : bond        0.03894 (  632)
  hydrogen bonds       : angle       4.78756 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1748 (tpp) cc_final: 0.1503 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1192
  time to fit residues: 10.3900
Evaluate side-chains
  34 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 131 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 140 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 88 optimal weight:    5.9990
   chunk 132 optimal weight:    3.9990
   chunk 138 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 518 GLN
C 521 GLN
C 542 GLN
E 230 ASN
E 314 GLN
** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.089219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.071356 restraints weight = 56543.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.069828 restraints weight = 66506.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.070351 restraints weight = 69705.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.070880 restraints weight = 44485.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.070986 restraints weight = 40947.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070  11535  Z= 0.307
  Angle     :  0.749   9.062  15604  Z= 0.380
  Chirality :  0.045   0.170   1771
  Planarity :  0.005   0.051   2081
  Dihedral  :  5.220  25.815   1613
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  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 aren not related in a simple way.
  whole:  0.05 (0.22), residues: 1461
  helix:  1.02 (0.18), residues: 764
  sheet: -1.25 (0.43), residues: 161
  loop : -0.89 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 227 
 TYR   0.028   0.003   TYR B 205 
 PHE   0.021   0.002   PHE B 211 
 TRP   0.005   0.001   TRP C 537 
 HIS   0.005   0.001   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00705 (11535)
  covalent geometry    : angle       0.74948 (15604)
  hydrogen bonds       : bond        0.04526 (  632)
  hydrogen bonds       : angle       5.23691 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1883 (tpp) cc_final: 0.1656 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1028
  time to fit residues: 6.5830
Evaluate side-chains
  32 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 358 GLN
E 230 ASN
** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.092516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.074613 restraints weight = 56131.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.072723 restraints weight = 62205.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.073503 restraints weight = 60143.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.073813 restraints weight = 40278.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.073934 restraints weight = 39459.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11535  Z= 0.122
  Angle     :  0.576   7.268  15604  Z= 0.290
  Chirality :  0.041   0.168   1771
  Planarity :  0.004   0.041   2081
  Dihedral  :  4.575  21.367   1613
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  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 aren not related in a simple way.
  whole:  0.44 (0.22), residues: 1461
  helix:  1.33 (0.18), residues: 775
  sheet: -0.89 (0.44), residues: 155
  loop : -0.83 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 227 
 TYR   0.017   0.001   TYR C  54 
 PHE   0.009   0.001   PHE B 104 
 TRP   0.009   0.001   TRP C 537 
 HIS   0.002   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (11535)
  covalent geometry    : angle       0.57645 (15604)
  hydrogen bonds       : bond        0.03645 (  632)
  hydrogen bonds       : angle       4.62679 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1696 (tpp) cc_final: 0.1199 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0981
  time to fit residues: 6.9748
Evaluate side-chains
  34 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 133 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 139 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 121 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 120 optimal weight:   20.0000
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:   20.0000
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 250 HIS
C 521 GLN
E 230 ASN
** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.093709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.072674 restraints weight = 57612.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.071433 restraints weight = 43243.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.071689 restraints weight = 44101.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.071832 restraints weight = 36811.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.071979 restraints weight = 33130.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11535  Z= 0.123
  Angle     :  0.559   6.549  15604  Z= 0.283
  Chirality :  0.041   0.142   1771
  Planarity :  0.004   0.039   2081
  Dihedral  :  4.409  20.329   1613
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  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 aren not related in a simple way.
  whole:  0.50 (0.22), residues: 1461
  helix:  1.39 (0.18), residues: 778
  sheet: -0.92 (0.42), residues: 164
  loop : -0.80 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 227 
 TYR   0.016   0.001   TYR B 205 
 PHE   0.008   0.001   PHE B 104 
 TRP   0.004   0.001   TRP C 304 
 HIS   0.001   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11535)
  covalent geometry    : angle       0.55922 (15604)
  hydrogen bonds       : bond        0.03527 (  632)
  hydrogen bonds       : angle       4.52296 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.0972 (tpp) cc_final: 0.0597 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1047
  time to fit residues: 7.4787
Evaluate side-chains
  32 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 121 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
B 312 GLN
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 521 GLN
E 230 ASN
** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.090533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.072657 restraints weight = 56271.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.071037 restraints weight = 63972.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.071588 restraints weight = 64763.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.072051 restraints weight = 41464.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.072148 restraints weight = 38994.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11535  Z= 0.214
  Angle     :  0.638   9.281  15604  Z= 0.324
  Chirality :  0.043   0.139   1771
  Planarity :  0.005   0.049   2081
  Dihedral  :  4.755  22.673   1613
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  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 aren not related in a simple way.
  whole:  0.31 (0.22), residues: 1461
  helix:  1.26 (0.18), residues: 772
  sheet: -1.06 (0.43), residues: 154
  loop : -0.89 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 382 
 TYR   0.045   0.002   TYR C 393 
 PHE   0.016   0.002   PHE B 211 
 TRP   0.003   0.001   TRP C 537 
 HIS   0.003   0.001   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (11535)
  covalent geometry    : angle       0.63759 (15604)
  hydrogen bonds       : bond        0.03952 (  632)
  hydrogen bonds       : angle       4.73051 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1741 (tpp) cc_final: 0.0742 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0793
  time to fit residues: 4.8824
Evaluate side-chains
  31 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0870
   chunk 99 optimal weight:    7.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.1560

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

Flipped N/Q/H residues before XYZ refinement:
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 521 GLN
E 230 ASN
** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.091826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.073708 restraints weight = 55929.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.071741 restraints weight = 61929.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.072527 restraints weight = 62229.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.072926 restraints weight = 40593.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.073075 restraints weight = 40039.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11535  Z= 0.148
  Angle     :  0.582   7.145  15604  Z= 0.293
  Chirality :  0.041   0.155   1771
  Planarity :  0.005   0.041   2081
  Dihedral  :  4.577  21.492   1613
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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 aren not related in a simple way.
  whole:  0.35 (0.22), residues: 1461
  helix:  1.33 (0.18), residues: 773
  sheet: -1.09 (0.42), residues: 163
  loop : -0.91 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 227 
 TYR   0.029   0.002   TYR C 393 
 PHE   0.009   0.001   PHE A  49 
 TRP   0.004   0.001   TRP C 304 
 HIS   0.002   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (11535)
  covalent geometry    : angle       0.58195 (15604)
  hydrogen bonds       : bond        0.03702 (  632)
  hydrogen bonds       : angle       4.56071 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1227 (tpp) cc_final: 0.0699 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0967
  time to fit residues: 6.0858
Evaluate side-chains
  31 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 145 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 79 optimal weight:    0.8980
   chunk 114 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 358 GLN ** 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 = 0.4009 r_free = 0.4009 target = 0.094243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.075432 restraints weight = 54800.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.073320 restraints weight = 65746.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.073959 restraints weight = 62740.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.074231 restraints weight = 40788.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.074379 restraints weight = 38171.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11535  Z= 0.126
  Angle     :  0.561   8.019  15604  Z= 0.283
  Chirality :  0.041   0.144   1771
  Planarity :  0.004   0.041   2081
  Dihedral  :  4.391  20.256   1613
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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 aren not related in a simple way.
  whole:  0.46 (0.22), residues: 1461
  helix:  1.42 (0.19), residues: 773
  sheet: -0.97 (0.44), residues: 154
  loop : -0.90 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 227 
 TYR   0.023   0.002   TYR C 393 
 PHE   0.009   0.001   PHE B 104 
 TRP   0.006   0.001   TRP C 537 
 HIS   0.001   0.000   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (11535)
  covalent geometry    : angle       0.56087 (15604)
  hydrogen bonds       : bond        0.03515 (  632)
  hydrogen bonds       : angle       4.53038 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1190 (tpp) cc_final: 0.0676 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0975
  time to fit residues: 6.0936
Evaluate side-chains
  34 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 116 optimal weight:    3.9990
   chunk 105 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0070
   chunk 35 optimal weight:    0.9990
   chunk 138 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 521 GLN
** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 358 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.095061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.076555 restraints weight = 55735.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.074302 restraints weight = 66765.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.075053 restraints weight = 63050.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.075300 restraints weight = 40075.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.075408 restraints weight = 39361.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11535  Z= 0.114
  Angle     :  0.551   7.355  15604  Z= 0.278
  Chirality :  0.041   0.138   1771
  Planarity :  0.004   0.041   2081
  Dihedral  :  4.218  18.622   1613
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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 aren not related in a simple way.
  whole:  0.50 (0.22), residues: 1461
  helix:  1.46 (0.19), residues: 778
  sheet: -1.06 (0.44), residues: 157
  loop : -0.87 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 227 
 TYR   0.019   0.001   TYR C 393 
 PHE   0.008   0.001   PHE B 104 
 TRP   0.017   0.001   TRP C 537 
 HIS   0.001   0.000   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (11535)
  covalent geometry    : angle       0.55147 (15604)
  hydrogen bonds       : bond        0.03401 (  632)
  hydrogen bonds       : angle       4.42272 ( 1872)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1058 (tpp) cc_final: 0.0710 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1034
  time to fit residues: 6.9307
Evaluate side-chains
  34 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 139 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
C 122 GLN
C 521 GLN
C 542 GLN
** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.091329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.073929 restraints weight = 55912.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.072226 restraints weight = 65851.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.072837 restraints weight = 66827.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.073268 restraints weight = 43294.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.073414 restraints weight = 39544.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11535  Z= 0.193
  Angle     :  0.621   9.408  15604  Z= 0.315
  Chirality :  0.042   0.162   1771
  Planarity :  0.005   0.117   2081
  Dihedral  :  4.546  22.381   1613
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  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 aren not related in a simple way.
  whole:  0.35 (0.22), residues: 1461
  helix:  1.31 (0.18), residues: 776
  sheet: -1.06 (0.43), residues: 155
  loop : -0.91 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.030   0.001   ARG B 227 
 TYR   0.033   0.002   TYR B 203 
 PHE   0.015   0.002   PHE B 211 
 TRP   0.004   0.001   TRP C 537 
 HIS   0.003   0.001   HIS C 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (11535)
  covalent geometry    : angle       0.62082 (15604)
  hydrogen bonds       : bond        0.03781 (  632)
  hydrogen bonds       : angle       4.62113 ( 1872)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1453.58 seconds
wall clock time: 26 minutes 7.90 seconds (1567.90 seconds total)