Starting phenix.real_space_refine
on Wed May 14 04:55:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxg_40851/05_2025/8sxg_40851.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxg_40851/05_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_40851/05_2025/8sxg_40851.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxg_40851/05_2025/8sxg_40851.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxg_40851/05_2025/8sxg_40851.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxg_40851/05_2025/8sxg_40851.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.047
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.75, per 1000 atoms: 0.59
  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: 2.79
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.21
  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: 3.85

  Time building geometry restraints manager: 3.23 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:             1.890
  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:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.320
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  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:             0.020
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.990
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (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
 TRP   0.004   0.001   TRP C 537 
 HIS   0.006   0.001   HIS C 325 
 PHE   0.010   0.001   PHE C 326 
 TYR   0.012   0.001   TYR C  54 
 ARG   0.003   0.000   ARG C 340 

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

*********************** 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  : 1.215 
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: 0.2935
  time to fit residues: 27.4384
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  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    8.9990
   chunk 110 optimal weight:    8.9990
   chunk 61 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   chunk 44 optimal weight:    0.4980
   chunk 69 optimal weight:    0.0060
   chunk 85 optimal weight:    3.9990
   chunk 132 optimal weight:    2.9990
   overall best weight:    0.7998

-------------------------------------------------------------------------------
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 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 358 GLN
E 396 ASN
E 422 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.095276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.076536 restraints weight = 54601.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.073817 restraints weight = 64342.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.074519 restraints weight = 62617.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11535  Z= 0.131
  Angle     :  0.559   6.196  15604  Z= 0.289
  Chirality :  0.041   0.144   1771
  Planarity :  0.004   0.036   2081
  Dihedral  :  4.248  19.740   1613
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  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:  0.94 (0.22), residues: 1461
  helix:  1.84 (0.19), residues: 763
  sheet: -0.83 (0.43), residues: 166
  loop : -0.65 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 537 
 HIS   0.003   0.001   HIS C 218 
 PHE   0.009   0.001   PHE B 104 
 TYR   0.017   0.002   TYR C  54 
 ARG   0.006   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03995 (  632)
  hydrogen bonds       : angle       4.71786 ( 1872)
  covalent geometry    : bond        0.00292 (11535)
  covalent geometry    : angle       0.55946 (15604)

*********************** 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
  58 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1313 (tpp) cc_final: 0.1060 (tpp)
REVERT: E  265 ILE cc_start: 0.8560 (mm) cc_final: 0.8160 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2605
  time to fit residues: 22.5393
Evaluate side-chains
  40 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0980
   chunk 30 optimal weight:    0.0000
   chunk 54 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 136 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 124 optimal weight:    0.7980
   chunk 145 optimal weight:    0.8980
   overall best weight:    0.4784

-------------------------------------------------------------------------------
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 153 HIS
C 335 GLN
** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 230 ASN
E 422 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.094371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.076658 restraints weight = 55979.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.075107 restraints weight = 60357.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.075761 restraints weight = 60846.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1843

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= 0.111
  Angle     :  0.538   6.250  15604  Z= 0.272
  Chirality :  0.040   0.139   1771
  Planarity :  0.004   0.037   2081
  Dihedral  :  4.138  18.816   1613
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  4.25 %
    Favored  : 95.58 %
  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:  0.98 (0.23), residues: 1461
  helix:  1.83 (0.19), residues: 768
  sheet: -0.87 (0.42), residues: 174
  loop : -0.54 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 410 
 HIS   0.001   0.000   HIS C 218 
 PHE   0.016   0.001   PHE C 176 
 TYR   0.014   0.001   TYR B 205 
 ARG   0.006   0.000   ARG C 437 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  632)
  hydrogen bonds       : angle       4.39619 ( 1872)
  covalent geometry    : bond        0.00241 (11535)
  covalent geometry    : angle       0.53780 (15604)

*********************** 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: 2
    poor density    : 56
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  153 HIS cc_start: 0.4628 (OUTLIER) cc_final: 0.4359 (m-70)
REVERT: C  432 MET cc_start: 0.1426 (tpp) cc_final: 0.1151 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2592
  time to fit residues: 22.1263
Evaluate side-chains
  42 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 142 optimal weight:   10.0000
   chunk 2 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 120 optimal weight:   30.0000
   chunk 66 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 147 ASN
C 335 GLN
** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 230 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.093436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.075115 restraints weight = 56004.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.073435 restraints weight = 59867.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.074156 restraints weight = 59793.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11535  Z= 0.140
  Angle     :  0.563  11.528  15604  Z= 0.284
  Chirality :  0.040   0.146   1771
  Planarity :  0.005   0.109   2081
  Dihedral  :  4.301  19.835   1613
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.34
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.22), residues: 1461
  helix:  1.69 (0.19), residues: 768
  sheet: -1.01 (0.41), residues: 180
  loop : -0.45 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 304 
 HIS   0.007   0.001   HIS C 153 
 PHE   0.010   0.001   PHE C 176 
 TYR   0.019   0.002   TYR B 205 
 ARG   0.014   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03642 (  632)
  hydrogen bonds       : angle       4.37403 ( 1872)
  covalent geometry    : bond        0.00320 (11535)
  covalent geometry    : angle       0.56347 (15604)

*********************** 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
  51 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1623 (tpp) cc_final: 0.1395 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2432
  time to fit residues: 18.8247
Evaluate side-chains
  39 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 141 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 125 optimal weight:    0.0980
   chunk 60 optimal weight:    0.0980
   chunk 15 optimal weight:    0.0010
   chunk 49 optimal weight:    0.6980
   chunk 142 optimal weight:    7.9990
   chunk 113 optimal weight:    0.0670
   chunk 10 optimal weight:   20.0000
   overall best weight:    0.1924

-------------------------------------------------------------------------------
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  64 GLN
** C 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.095378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.077005 restraints weight = 55664.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.075252 restraints weight = 55060.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.076070 restraints weight = 53193.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11535  Z= 0.101
  Angle     :  0.534  10.395  15604  Z= 0.266
  Chirality :  0.039   0.151   1771
  Planarity :  0.004   0.054   2081
  Dihedral  :  4.051  17.289   1613
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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:  0.90 (0.22), residues: 1461
  helix:  1.72 (0.18), residues: 767
  sheet: -0.95 (0.41), residues: 182
  loop : -0.45 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 304 
 HIS   0.001   0.000   HIS C 325 
 PHE   0.009   0.001   PHE B 104 
 TYR   0.016   0.001   TYR B 203 
 ARG   0.009   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03326 (  632)
  hydrogen bonds       : angle       4.17733 ( 1872)
  covalent geometry    : bond        0.00209 (11535)
  covalent geometry    : angle       0.53426 (15604)

*********************** 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
  58 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1596 (tpp) cc_final: 0.1129 (tpp)
REVERT: E  265 ILE cc_start: 0.8556 (mm) cc_final: 0.8118 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2494
  time to fit residues: 21.7852
Evaluate side-chains
  40 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 103 optimal weight:   20.0000
   chunk 111 optimal weight:   20.0000
   chunk 42 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 139 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.8682

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.093958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.075384 restraints weight = 56724.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.073960 restraints weight = 53815.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.074556 restraints weight = 54402.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11535  Z= 0.123
  Angle     :  0.535   8.440  15604  Z= 0.269
  Chirality :  0.040   0.158   1771
  Planarity :  0.004   0.040   2081
  Dihedral  :  4.121  18.569   1613
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  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:  0.87 (0.22), residues: 1461
  helix:  1.69 (0.18), residues: 768
  sheet: -0.91 (0.41), residues: 179
  loop : -0.49 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP C 304 
 HIS   0.001   0.000   HIS C 250 
 PHE   0.008   0.001   PHE B 104 
 TYR   0.018   0.001   TYR B 205 
 ARG   0.006   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (  632)
  hydrogen bonds       : angle       4.19405 ( 1872)
  covalent geometry    : bond        0.00279 (11535)
  covalent geometry    : angle       0.53494 (15604)

*********************** 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
  46 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1647 (tpp) cc_final: 0.1175 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.2267
  time to fit residues: 16.3188
Evaluate side-chains
  39 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 8 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 121 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 149 GLN
** E 230 ASN ** 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 = 0.4006 r_free = 0.4006 target = 0.092987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.074795 restraints weight = 56896.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.073047 restraints weight = 63616.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.073768 restraints weight = 63345.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11535  Z= 0.153
  Angle     :  0.563   7.427  15604  Z= 0.285
  Chirality :  0.041   0.158   1771
  Planarity :  0.004   0.040   2081
  Dihedral  :  4.292  19.983   1613
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  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:  0.73 (0.22), residues: 1461
  helix:  1.55 (0.18), residues: 770
  sheet: -0.99 (0.41), residues: 178
  loop : -0.52 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 304 
 HIS   0.002   0.000   HIS C 250 
 PHE   0.010   0.001   PHE B 211 
 TYR   0.021   0.002   TYR B 205 
 ARG   0.006   0.000   ARG C 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  632)
  hydrogen bonds       : angle       4.33955 ( 1872)
  covalent geometry    : bond        0.00350 (11535)
  covalent geometry    : angle       0.56252 (15604)

*********************** 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
  45 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  149 GLN cc_start: 0.7423 (mp-120) cc_final: 0.6725 (mp10)
REVERT: C  432 MET cc_start: 0.1658 (tpp) cc_final: 0.1186 (tpp)
REVERT: C  440 LEU cc_start: 0.6444 (mt) cc_final: 0.6114 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.2435
  time to fit residues: 18.0334
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  : 1.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 144 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 133 optimal weight:    3.9990
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.093779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.075458 restraints weight = 56623.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.073714 restraints weight = 58346.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.074520 restraints weight = 58164.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11535  Z= 0.123
  Angle     :  0.540   7.110  15604  Z= 0.272
  Chirality :  0.040   0.140   1771
  Planarity :  0.004   0.040   2081
  Dihedral  :  4.225  20.412   1613
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.22), residues: 1461
  helix:  1.57 (0.18), residues: 771
  sheet: -1.04 (0.41), residues: 178
  loop : -0.53 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 304 
 HIS   0.001   0.000   HIS C 486 
 PHE   0.008   0.001   PHE B 104 
 TYR   0.018   0.001   TYR B 203 
 ARG   0.005   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  632)
  hydrogen bonds       : angle       4.24079 ( 1872)
  covalent geometry    : bond        0.00281 (11535)
  covalent geometry    : angle       0.54043 (15604)

*********************** 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
  47 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.0908 (tpp) cc_final: 0.0402 (mtp)
REVERT: C  440 LEU cc_start: 0.6506 (mt) cc_final: 0.6150 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.2623
  time to fit residues: 18.4049
Evaluate side-chains
  36 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 118 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 138 optimal weight:    0.0070
   chunk 107 optimal weight:    6.9990
   chunk 139 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   overall best weight:    1.4802

-------------------------------------------------------------------------------
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 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 218 HIS
** E 230 ASN ** 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 = 0.3996 r_free = 0.3996 target = 0.093545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.072003 restraints weight = 57641.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.070420 restraints weight = 43914.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.070642 restraints weight = 47029.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11535  Z= 0.169
  Angle     :  0.587   6.396  15604  Z= 0.295
  Chirality :  0.041   0.137   1771
  Planarity :  0.004   0.060   2081
  Dihedral  :  4.433  21.138   1613
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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:  0.61 (0.22), residues: 1461
  helix:  1.47 (0.18), residues: 772
  sheet: -1.00 (0.42), residues: 171
  loop : -0.64 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 304 
 HIS   0.002   0.001   HIS C 218 
 PHE   0.013   0.001   PHE B 211 
 TYR   0.020   0.002   TYR B 205 
 ARG   0.004   0.000   ARG C 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  632)
  hydrogen bonds       : angle       4.37436 ( 1872)
  covalent geometry    : bond        0.00389 (11535)
  covalent geometry    : angle       0.58671 (15604)

*********************** 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
  44 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.0981 (tpp) cc_final: 0.0742 (mtp)
REVERT: C  440 LEU cc_start: 0.7014 (mt) cc_final: 0.6587 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2200
  time to fit residues: 15.4899
Evaluate side-chains
  37 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 79 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 142 optimal weight:    5.9990
   chunk 117 optimal weight:    8.9990
   chunk 120 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0770
   chunk 119 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.7542

-------------------------------------------------------------------------------
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  64 GLN
** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 230 ASN ** 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 = 0.4023 r_free = 0.4023 target = 0.093715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.075536 restraints weight = 55966.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.073954 restraints weight = 61416.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.074695 restraints weight = 60329.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11535  Z= 0.119
  Angle     :  0.544   6.657  15604  Z= 0.273
  Chirality :  0.040   0.141   1771
  Planarity :  0.004   0.040   2081
  Dihedral  :  4.251  19.623   1613
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  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:  0.64 (0.22), residues: 1461
  helix:  1.51 (0.18), residues: 776
  sheet: -1.03 (0.41), residues: 173
  loop : -0.64 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 304 
 HIS   0.002   0.000   HIS C 325 
 PHE   0.008   0.001   PHE B 104 
 TYR   0.015   0.001   TYR B 205 
 ARG   0.005   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  632)
  hydrogen bonds       : angle       4.25117 ( 1872)
  covalent geometry    : bond        0.00269 (11535)
  covalent geometry    : angle       0.54433 (15604)

********************** 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
  44 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  432 MET cc_start: 0.1087 (tpp) cc_final: 0.0737 (mtp)
REVERT: C  440 LEU cc_start: 0.6452 (mt) cc_final: 0.6124 (tp)
REVERT: E  265 ILE cc_start: 0.8609 (mm) cc_final: 0.8255 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2232
  time to fit residues: 15.6067
Evaluate side-chains
  37 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 75 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 127 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 218 HIS
** E 230 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.095520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.076793 restraints weight = 54888.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.074694 restraints weight = 66105.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.075327 restraints weight = 62864.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11535  Z= 0.118
  Angle     :  0.539   8.513  15604  Z= 0.269
  Chirality :  0.040   0.140   1771
  Planarity :  0.004   0.040   2081
  Dihedral  :  4.163  19.155   1613
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.22), residues: 1461
  helix:  1.57 (0.18), residues: 776
  sheet: -1.03 (0.41), residues: 173
  loop : -0.67 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 304 
 HIS   0.003   0.001   HIS C 218 
 PHE   0.007   0.001   PHE B 104 
 TYR   0.016   0.001   TYR B 205 
 ARG   0.006   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  632)
  hydrogen bonds       : angle       4.20438 ( 1872)
  covalent geometry    : bond        0.00267 (11535)
  covalent geometry    : angle       0.53902 (15604)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2944.88 seconds
wall clock time: 53 minutes 10.47 seconds (3190.47 seconds total)