Starting phenix.real_space_refine
on Fri Feb 14 12:23:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sz9_10350/02_2025/6sz9_10350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sz9_10350/02_2025/6sz9_10350.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sz9_10350/02_2025/6sz9_10350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sz9_10350/02_2025/6sz9_10350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sz9_10350/02_2025/6sz9_10350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sz9_10350/02_2025/6sz9_10350.cif"
  }
  resolution = 3.7
  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=   0.841
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      48      5.16       5
     C    6520      2.51       5
     N    1748      2.21       5
     O    1916      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10233
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3665
          Classifications: {'peptide': 473}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 19, 'TRANS': 453}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "B"
      Number of atoms: 2085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2085
          Classifications: {'peptide': 259}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 241}
    Chain: "C"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1615
          Classifications: {'peptide': 202}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 197}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 2284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2284
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 275}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 583
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6091  SG  CYS C  46      72.511  31.236  60.268  1.00 35.96           S
  ATOM   6117  SG  CYS C  49      75.680  32.328  60.598  1.00 29.67           S
  ATOM   6346  SG  CYS C  78      73.743  35.280  59.358  1.00 29.81           S
  ATOM   6369  SG  CYS C  81      74.403  32.503  57.235  1.00 27.56           S

  Time building chain proxies: 5.53, per 1000 atoms: 0.54
  Number of scatterers: 10233
  At special positions: 0
  Unit cell: (119.13, 110.77, 122.265, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      48     16.00
     O    1916      8.00
     N    1748      7.00
     C    6520      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: 2.53
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 301 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  46 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  81 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  49 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  78 "
      Number of angles added : 6


  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2444

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      59.5% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 3.702A  pdb=" N   THR A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 152
      removed outlier: 3.701A  pdb=" N   THR A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 178
    Processing helix  chain 'A' and resid 218 through 228
    Processing helix  chain 'A' and resid 240 through 262
      removed outlier: 3.939A  pdb=" N   GLU A 261 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 3.833A  pdb=" N   ILE A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 285
    Processing helix  chain 'A' and resid 303 through 316
      removed outlier: 4.063A  pdb=" N   THR A 307 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      Proline residue:  A 309  - end of helix
    Processing helix  chain 'A' and resid 325 through 353
      removed outlier: 4.123A  pdb=" N   SER A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   GLU A 334 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   GLN A 335 " --> pdb=" O   GLN A 331 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   GLN A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   LEU A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 374
      removed outlier: 3.537A  pdb=" N   VAL A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 408
      removed outlier: 4.264A  pdb=" N   LEU A 391 " --> pdb=" O   SER A 387 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 459
      removed outlier: 3.714A  pdb=" N   GLY A 459 " --> pdb=" O   ARG A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 476
    Processing helix  chain 'A' and resid 479 through 487
    Processing helix  chain 'A' and resid 594 through 615
      removed outlier: 3.677A  pdb=" N   MET A 599 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LYS A 600 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER A 610 " --> pdb=" O   ALA A 606 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE A 611 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLY A 615 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
      removed outlier: 3.795A  pdb=" N   SER A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 658
    Processing helix  chain 'B' and resid 126 through 134
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 3.664A  pdb=" N   ILE B 141 " --> pdb=" O   TRP B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 172
    Processing helix  chain 'B' and resid 196 through 207
      removed outlier: 4.057A  pdb=" N   ARG B 202 " --> pdb=" O   GLY B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 234
      removed outlier: 3.550A  pdb=" N   ASN B 234 " --> pdb=" O   MET B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 253
      removed outlier: 3.729A  pdb=" N   ALA B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 260
      No H-bonds generated for 'chain 'B' and resid 258 through 260'
    Processing helix  chain 'B' and resid 261 through 266
      removed outlier: 3.637A  pdb=" N   MET B 265 " --> pdb=" O   ALA B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 280
    Processing helix  chain 'B' and resid 283 through 296
    Processing helix  chain 'B' and resid 297 through 299
      No H-bonds generated for 'chain 'B' and resid 297 through 299'
    Processing helix  chain 'B' and resid 302 through 306
      removed outlier: 3.858A  pdb=" N   GLU B 305 " --> pdb=" O   PRO B 302 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   PHE B 306 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 302 through 306'
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.998A  pdb=" N   VAL B 312 " --> pdb=" O   TRP B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 323
      removed outlier: 3.532A  pdb=" N   VAL B 323 " --> pdb=" O   MET B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 346
      removed outlier: 3.755A  pdb=" N   MET B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 346 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 366
      removed outlier: 4.311A  pdb=" N   ARG B 359 " --> pdb=" O   ASP B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 376
    Processing helix  chain 'C' and resid 18 through 28
      removed outlier: 3.789A  pdb=" N   ILE C  27 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ASP C  28 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 43
      removed outlier: 3.530A  pdb=" N   LYS C  32 " --> pdb=" O   ASP C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 84
    Processing helix  chain 'C' and resid 107 through 123
    Processing helix  chain 'C' and resid 128 through 151
      removed outlier: 3.620A  pdb=" N   ALA C 132 " --> pdb=" O   TYR C 128 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER C 138 " --> pdb=" O   ASN C 134 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLU C 147 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLU C 148 " --> pdb=" O   GLN C 144 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LYS C 149 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 166
    Processing helix  chain 'C' and resid 171 through 179
    Processing helix  chain 'C' and resid 191 through 207
      removed outlier: 3.523A  pdb=" N   ALA C 207 " --> pdb=" O   LEU C 203 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 29
    Processing helix  chain 'D' and resid 36 through 42
    Processing helix  chain 'D' and resid 48 through 85
      removed outlier: 4.499A  pdb=" N   ILE D  55 " --> pdb=" O   HIS D  51 " (cutoff:3.500A)
      Proline residue:  D  56  - end of helix
      removed outlier: 3.754A  pdb=" N   ASN D  59 " --> pdb=" O   ILE D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 159
      removed outlier: 4.106A  pdb=" N   GLU D 102 " --> pdb=" O   ALA D  98 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   SER D 103 " --> pdb=" O   GLY D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 181
      removed outlier: 3.620A  pdb=" N   CYS D 181 " --> pdb=" O   ALA D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 203
      removed outlier: 4.101A  pdb=" N   LYS D 192 " --> pdb=" O   SER D 188 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   TYR D 193 " --> pdb=" O   GLN D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 266
      removed outlier: 5.421A  pdb=" N   GLU D 221 " --> pdb=" O   THR D 217 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   LEU D 222 " --> pdb=" O   ASN D 218 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR D 231 " --> pdb=" O   GLU D 227 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS D 232 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   HIS D 242 " --> pdb=" O   ASP D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 283
    Processing helix  chain 'E' and resid 8 through 19
      removed outlier: 3.713A  pdb=" N   GLY E  19 " --> pdb=" O   ALA E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 39
      removed outlier: 3.602A  pdb=" N   ALA E  26 " --> pdb=" O   SER E  22 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 64
    Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120
      removed outlier: 3.924A  pdb=" N   GLY A 109 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   PHE A 120 " --> pdb=" O   PHE A 107 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   PHE A 107 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ALA A 558 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   PHE A 464 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 466 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189
      removed outlier: 6.407A  pdb=" N   LEU A 186 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   LEU A 380 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE A 188 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   TYR A 159 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289
      removed outlier: 3.715A  pdb=" N   VAL A 297 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 176
    Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 60
    Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 101

    521 hydrogen bonds defined for protein.
    1542 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: 3.07

  Time building geometry restraints manager: 2.92 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: 3327
        1.34 -     1.46: 1857
        1.46 -     1.58: 5151
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 10415
  Sorted by residual:
  bond pdb=" N   PHE C  48 "
       pdb=" CA  PHE C  48 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.25e+00
  bond pdb=" N   CYS C  78 "
       pdb=" CA  CYS C  78 "
    ideal  model  delta    sigma   weight residual
    1.453  1.485 -0.033 1.31e-02 5.83e+03 6.20e+00
  bond pdb=" N   CYS C  49 "
       pdb=" CA  CYS C  49 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.50e-02 4.44e+03 5.57e+00
  bond pdb=" N   GLN C  47 "
       pdb=" CA  GLN C  47 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.57e+00
  bond pdb=" N   GLY C  50 "
       pdb=" CA  GLY C  50 "
    ideal  model  delta    sigma   weight residual
    1.446  1.479 -0.032 1.50e-02 4.44e+03 4.68e+00
  ... (remaining 10410 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 13527
        1.90 -     3.80: 469
        3.80 -     5.71: 39
        5.71 -     7.61: 16
        7.61 -     9.51: 7
  Bond angle restraints: 14058
  Sorted by residual:
  angle pdb=" C   ASP A 286 "
        pdb=" N   LYS A 287 "
        pdb=" CA  LYS A 287 "
      ideal   model   delta    sigma   weight residual
     122.07  127.34   -5.27 1.43e+00 4.89e-01 1.36e+01
  angle pdb=" C   TYR D  29 "
        pdb=" N   ASN D  30 "
        pdb=" CA  ASN D  30 "
      ideal   model   delta    sigma   weight residual
     122.40  127.55   -5.15 1.45e+00 4.76e-01 1.26e+01
  angle pdb=" N   ASP A 308 "
        pdb=" CA  ASP A 308 "
        pdb=" C   ASP A 308 "
      ideal   model   delta    sigma   weight residual
     109.81  116.73   -6.92 2.21e+00 2.05e-01 9.81e+00
  angle pdb=" CA  LYS A 287 "
        pdb=" CB  LYS A 287 "
        pdb=" CG  LYS A 287 "
      ideal   model   delta    sigma   weight residual
     114.10  120.31   -6.21 2.00e+00 2.50e-01 9.65e+00
  angle pdb=" CA  CYS C  79 "
        pdb=" C   CYS C  79 "
        pdb=" O   CYS C  79 "
      ideal   model   delta    sigma   weight residual
     120.55  117.34    3.21 1.06e+00 8.90e-01 9.15e+00
  ... (remaining 14053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 5605
       17.86 -    35.71: 642
       35.71 -    53.56: 100
       53.56 -    71.42: 24
       71.42 -    89.27: 11
  Dihedral angle restraints: 6382
    sinusoidal: 2612
      harmonic: 3770
  Sorted by residual:
  dihedral pdb=" CA  GLU A 591 "
           pdb=" C   GLU A 591 "
           pdb=" N   PRO A 592 "
           pdb=" CA  PRO A 592 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  LYS A 474 "
           pdb=" C   LYS A 474 "
           pdb=" N   ALA A 475 "
           pdb=" CA  ALA A 475 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.42  -19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  ASP A 366 "
           pdb=" C   ASP A 366 "
           pdb=" N   PHE A 367 "
           pdb=" CA  PHE A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.81  -19.19     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 6379 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1244
       0.056 -    0.111: 280
       0.111 -    0.167: 45
       0.167 -    0.223: 9
       0.223 -    0.278: 3
  Chirality restraints: 1581
  Sorted by residual:
  chirality pdb=" CB  VAL A 332 "
            pdb=" CA  VAL A 332 "
            pdb=" CG1 VAL A 332 "
            pdb=" CG2 VAL A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CB  ILE A 131 "
            pdb=" CA  ILE A 131 "
            pdb=" CG1 ILE A 131 "
            pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  ILE D  44 "
            pdb=" CA  ILE D  44 "
            pdb=" CG1 ILE D  44 "
            pdb=" CG2 ILE D  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1578 not shown)

  Planarity restraints: 1809
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  44 "   -0.040 5.00e-02 4.00e+02   6.04e-02 5.84e+00
        pdb=" N   PRO D  45 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO D  45 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  45 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 289 "    0.036 5.00e-02 4.00e+02   5.38e-02 4.64e+00
        pdb=" N   PRO A 290 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 362 "   -0.011 2.00e-02 2.50e+03   2.12e-02 4.50e+00
        pdb=" C   GLU B 362 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU B 362 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE B 363 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1806 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2983
        2.81 -     3.34: 9194
        3.34 -     3.86: 16595
        3.86 -     4.38: 18277
        4.38 -     4.90: 31998
  Nonbonded interactions: 79047
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 114 "
            pdb=" OE1 GLU A 116 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ALA A 150 "
            pdb=" OG  SER A 155 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ILE A 483 "
            pdb=" OG1 THR A 487 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ASP D  82 "
            pdb=" OH  TYR D 271 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OD1 ASN C 124 "
            pdb=" OG1 THR D  21 "
     model   vdw
     2.319 3.040
  ... (remaining 79042 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.690
  Find NCS groups from input model:        0.110
  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:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  10415  Z= 0.295
  Angle     :  0.817   9.511  14058  Z= 0.459
  Chirality :  0.050   0.278   1581
  Planarity :  0.006   0.060   1809
  Dihedral  : 15.573  89.271   3938
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  9.90 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.18), residues: 1274
  helix: -2.19 (0.15), residues: 717
  sheet: -2.04 (0.69), residues: 54
  loop : -2.96 (0.22), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 159 
 HIS   0.005   0.001   HIS B 281 
 PHE   0.027   0.002   PHE D 254 
 TYR   0.025   0.002   TYR A 440 
 ARG   0.005   0.000   ARG B 296 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 MET cc_start: 0.8440 (ttm) cc_final: 0.8230 (ttm)
REVERT: A  179 MET cc_start: 0.8538 (mmm) cc_final: 0.8014 (mmt)
REVERT: A  240 TRP cc_start: 0.5607 (m-10) cc_final: 0.4781 (p90)
REVERT: A  266 LEU cc_start: 0.8524 (tp) cc_final: 0.8321 (tp)
REVERT: A  405 MET cc_start: 0.6748 (mtp) cc_final: 0.6373 (mtp)
REVERT: B  145 VAL cc_start: 0.8790 (p) cc_final: 0.8579 (m)
REVERT: B  161 MET cc_start: 0.7753 (ttp) cc_final: 0.7014 (ttp)
REVERT: B  173 ASN cc_start: 0.8364 (m-40) cc_final: 0.7971 (t0)
REVERT: B  363 ILE cc_start: 0.8738 (mm) cc_final: 0.8218 (mt)
REVERT: C   10 LEU cc_start: 0.7938 (mt) cc_final: 0.7699 (mp)
REVERT: C  166 ASP cc_start: 0.8109 (t0) cc_final: 0.7807 (t0)
REVERT: D   66 ILE cc_start: 0.8906 (pt) cc_final: 0.8280 (mt)
REVERT: D   83 TYR cc_start: 0.7525 (t80) cc_final: 0.7234 (t80)
REVERT: E   27 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7448 (tm-30)
REVERT: E   28 TYR cc_start: 0.8689 (t80) cc_final: 0.8437 (t80)
REVERT: E   56 TYR cc_start: 0.7830 (t80) cc_final: 0.7147 (t80)
REVERT: E   63 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7638 (tptt)
REVERT: E   75 GLU cc_start: 0.8179 (pm20) cc_final: 0.7583 (mm-30)
REVERT: E   76 ARG cc_start: 0.6513 (mmm-85) cc_final: 0.6063 (mmt90)
  outliers start: 3
  outliers final: 2
  residues processed: 207
  average time/residue: 0.2479
  time to fit residues: 70.2787
Evaluate side-chains
  152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain B residue  300 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0010
   chunk 32 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 ASN
A 331 GLN
A 342 GLN
A 361 ASN
A 373 ASN
A 467 GLN
A 602 GLN
B 133 GLN
C  36 GLN
C  57 GLN
C 108 GLN
C 124 ASN
C 162 GLN
D  59 ASN
D  62 ASN
D 200 ASN
D 218 ASN
D 241 ASN
D 245 GLN
D 277 GLN
D 281 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.155626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.124880 restraints weight = 17494.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.128060 restraints weight = 11102.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.130128 restraints weight = 8380.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10415  Z= 0.193
  Angle     :  0.581   9.060  14058  Z= 0.302
  Chirality :  0.040   0.176   1581
  Planarity :  0.004   0.043   1809
  Dihedral  :  4.768  32.916   1400
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.58 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.22), residues: 1274
  helix: -0.35 (0.19), residues: 718
  sheet: -2.20 (0.59), residues: 66
  loop : -2.60 (0.24), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  71 
 HIS   0.005   0.001   HIS D 242 
 PHE   0.021   0.001   PHE C  31 
 TYR   0.012   0.001   TYR D  83 
 ARG   0.005   0.000   ARG A 243 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5519 (m-10) cc_final: 0.4676 (p90)
REVERT: A  252 MET cc_start: 0.7691 (mmp) cc_final: 0.7483 (mmp)
REVERT: A  405 MET cc_start: 0.7073 (mtp) cc_final: 0.6770 (mtp)
REVERT: B  173 ASN cc_start: 0.8294 (m-40) cc_final: 0.7939 (t0)
REVERT: B  189 GLU cc_start: 0.7472 (tt0) cc_final: 0.7218 (tt0)
REVERT: C   10 LEU cc_start: 0.7900 (mt) cc_final: 0.7556 (mp)
REVERT: C   62 LEU cc_start: 0.7131 (mt) cc_final: 0.6882 (mt)
REVERT: D   66 ILE cc_start: 0.8844 (pt) cc_final: 0.8227 (mt)
REVERT: E   12 LEU cc_start: 0.8828 (tt) cc_final: 0.8610 (mm)
REVERT: E   14 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8215 (mtpp)
REVERT: E   16 MET cc_start: 0.7796 (mmm) cc_final: 0.7583 (tpp)
REVERT: E   27 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7534 (tm-30)
REVERT: E   51 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: E   56 TYR cc_start: 0.7675 (t80) cc_final: 0.7469 (t80)
REVERT: E   62 PHE cc_start: 0.7164 (m-80) cc_final: 0.6697 (m-80)
REVERT: E   63 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7688 (tptt)
REVERT: E   75 GLU cc_start: 0.8130 (pm20) cc_final: 0.7617 (mm-30)
  outliers start: 20
  outliers final: 10
  residues processed: 172
  average time/residue: 0.2275
  time to fit residues: 55.2075
Evaluate side-chains
  151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain E residue   41 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0070
   chunk 113 optimal weight:    0.5980
   chunk 109 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.0400

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
C  36 GLN
C  57 GLN
D 277 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.153877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.122866 restraints weight = 17741.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.125938 restraints weight = 11602.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.127934 restraints weight = 8865.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10415  Z= 0.223
  Angle     :  0.571  10.204  14058  Z= 0.294
  Chirality :  0.040   0.167   1581
  Planarity :  0.004   0.035   1809
  Dihedral  :  4.585  33.345   1400
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.20 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.23), residues: 1274
  helix:  0.33 (0.19), residues: 718
  sheet: -1.85 (0.70), residues: 55
  loop : -2.31 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 119 
 HIS   0.004   0.001   HIS D 242 
 PHE   0.015   0.001   PHE C  31 
 TYR   0.009   0.001   TYR A 433 
 ARG   0.008   0.000   ARG E  76 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5529 (m-10) cc_final: 0.4572 (p90)
REVERT: A  252 MET cc_start: 0.7585 (mmp) cc_final: 0.7385 (mmp)
REVERT: A  405 MET cc_start: 0.6958 (mtp) cc_final: 0.6628 (mtp)
REVERT: B  173 ASN cc_start: 0.8284 (m-40) cc_final: 0.7860 (t0)
REVERT: D   66 ILE cc_start: 0.8867 (pt) cc_final: 0.8282 (mt)
REVERT: D  116 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7558 (t0)
REVERT: E   12 LEU cc_start: 0.8862 (tt) cc_final: 0.8633 (mm)
REVERT: E   14 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8272 (mtpp)
REVERT: E   27 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: E   55 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7821 (mt-10)
REVERT: E   62 PHE cc_start: 0.7370 (m-80) cc_final: 0.6804 (m-80)
REVERT: E   75 GLU cc_start: 0.7995 (pm20) cc_final: 0.7604 (mm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 163
  average time/residue: 0.2397
  time to fit residues: 54.6323
Evaluate side-chains
  156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain D residue  116 ASP
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 94 optimal weight:    0.0870
   chunk 30 optimal weight:    0.6980
   chunk 109 optimal weight:    0.0070
   chunk 56 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 114 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0980
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
A 336 HIS
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
C  57 GLN
D 253 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.156954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.126730 restraints weight = 17578.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.129854 restraints weight = 11234.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.131897 restraints weight = 8493.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
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      :  0.002   0.031  10415  Z= 0.150
  Angle     :  0.532   9.132  14058  Z= 0.272
  Chirality :  0.039   0.173   1581
  Planarity :  0.003   0.035   1809
  Dihedral  :  4.349  35.739   1400
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.38 %
    Favored  : 81.01 %
  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: -0.77 (0.23), residues: 1274
  helix:  0.75 (0.20), residues: 720
  sheet: -2.23 (0.61), residues: 66
  loop : -2.22 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.013   0.001   PHE C 179 
 TYR   0.015   0.001   TYR D  83 
 ARG   0.004   0.000   ARG A 570 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 160
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5632 (m-10) cc_final: 0.4659 (p90)
REVERT: A  291 ARG cc_start: 0.6427 (ttt180) cc_final: 0.6051 (ttt180)
REVERT: A  405 MET cc_start: 0.6714 (mtp) cc_final: 0.6420 (mtp)
REVERT: B  173 ASN cc_start: 0.8272 (m-40) cc_final: 0.7902 (t0)
REVERT: B  189 GLU cc_start: 0.7592 (tt0) cc_final: 0.7263 (tt0)
REVERT: B  265 MET cc_start: 0.8557 (tpp) cc_final: 0.8235 (tpt)
REVERT: D   66 ILE cc_start: 0.8872 (pt) cc_final: 0.8239 (mt)
REVERT: D  116 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7546 (t0)
REVERT: E   12 LEU cc_start: 0.8851 (tt) cc_final: 0.8640 (mm)
REVERT: E   14 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8292 (mtpp)
REVERT: E   16 MET cc_start: 0.7911 (tpt) cc_final: 0.7599 (tpt)
REVERT: E   27 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7556 (tm-30)
REVERT: E   51 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8205 (tm-30)
REVERT: E   56 TYR cc_start: 0.7978 (t80) cc_final: 0.7668 (t80)
REVERT: E   62 PHE cc_start: 0.7405 (m-80) cc_final: 0.6835 (m-80)
REVERT: E   63 LYS cc_start: 0.8704 (tttt) cc_final: 0.7835 (tptt)
REVERT: E   64 LEU cc_start: 0.8199 (mm) cc_final: 0.7998 (mm)
REVERT: E   75 GLU cc_start: 0.8038 (pm20) cc_final: 0.7583 (mm-30)
  outliers start: 29
  outliers final: 17
  residues processed: 179
  average time/residue: 0.2077
  time to fit residues: 53.8071
Evaluate side-chains
  162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain D residue  116 ASP
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 122 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0870
   chunk 23 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.5162

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 GLN
B 326 GLN
C  57 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.151961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.122181 restraints weight = 17665.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.124666 restraints weight = 12383.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.126332 restraints weight = 9896.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10415  Z= 0.291
  Angle     :  0.616   8.992  14058  Z= 0.311
  Chirality :  0.041   0.161   1581
  Planarity :  0.004   0.041   1809
  Dihedral  :  4.449  30.887   1398
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.00 %
    Favored  : 79.21 %
  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: 1274
  helix:  0.72 (0.20), residues: 721
  sheet: -2.02 (0.63), residues: 66
  loop : -2.24 (0.25), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 159 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.013   0.002   PHE C 160 
 TYR   0.024   0.002   TYR E  28 
 ARG   0.004   0.000   ARG E  32 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 1.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5536 (m-10) cc_final: 0.4503 (p90)
REVERT: A  291 ARG cc_start: 0.6560 (ttt180) cc_final: 0.6270 (tpt-90)
REVERT: A  405 MET cc_start: 0.6826 (mtp) cc_final: 0.6505 (mtp)
REVERT: B  173 ASN cc_start: 0.8301 (m-40) cc_final: 0.7927 (t0)
REVERT: B  265 MET cc_start: 0.8483 (tpp) cc_final: 0.8098 (tpt)
REVERT: D   66 ILE cc_start: 0.8920 (pt) cc_final: 0.8398 (mt)
REVERT: E   14 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8353 (mtpp)
REVERT: E   16 MET cc_start: 0.7965 (tpt) cc_final: 0.7470 (tpt)
REVERT: E   27 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7659 (tm-30)
REVERT: E   51 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8121 (tm-30)
REVERT: E   55 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7807 (mt-10)
REVERT: E   56 TYR cc_start: 0.8039 (t80) cc_final: 0.7524 (t80)
REVERT: E   62 PHE cc_start: 0.7429 (m-80) cc_final: 0.6961 (m-80)
REVERT: E   63 LYS cc_start: 0.8755 (tttt) cc_final: 0.7931 (tptt)
REVERT: E   75 GLU cc_start: 0.8094 (pm20) cc_final: 0.7644 (mm-30)
  outliers start: 31
  outliers final: 23
  residues processed: 164
  average time/residue: 0.2232
  time to fit residues: 52.2680
Evaluate side-chains
  158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 120 optimal weight:    8.9990
   chunk 77 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 85 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
C  36 GLN
C  57 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.154412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123755 restraints weight = 17598.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.126769 restraints weight = 11337.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.128465 restraints weight = 8668.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10415  Z= 0.183
  Angle     :  0.566   8.645  14058  Z= 0.282
  Chirality :  0.039   0.161   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.319  33.398   1398
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.09 %
    Favored  : 78.94 %
  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: -0.51 (0.24), residues: 1274
  helix:  0.97 (0.20), residues: 720
  sheet: -2.06 (0.62), residues: 66
  loop : -2.14 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 119 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.009   0.001   PHE A 347 
 TYR   0.015   0.001   TYR D  83 
 ARG   0.003   0.000   ARG A 112 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  240 TRP cc_start: 0.5581 (m-10) cc_final: 0.4484 (p90)
REVERT: A  291 ARG cc_start: 0.6535 (ttt180) cc_final: 0.6222 (tpt-90)
REVERT: A  405 MET cc_start: 0.6739 (mtp) cc_final: 0.6458 (mtp)
REVERT: B  173 ASN cc_start: 0.8289 (m-40) cc_final: 0.7922 (t0)
REVERT: B  265 MET cc_start: 0.8443 (tpp) cc_final: 0.8077 (tpt)
REVERT: D   66 ILE cc_start: 0.8897 (pt) cc_final: 0.8271 (mt)
REVERT: D  116 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7561 (t0)
REVERT: E   14 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8323 (mtpp)
REVERT: E   27 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: E   56 TYR cc_start: 0.7979 (t80) cc_final: 0.7459 (t80)
REVERT: E   62 PHE cc_start: 0.7422 (m-80) cc_final: 0.6935 (m-80)
REVERT: E   63 LYS cc_start: 0.8773 (tttt) cc_final: 0.7887 (tptt)
REVERT: E   75 GLU cc_start: 0.8053 (pm20) cc_final: 0.7666 (mm-30)
  outliers start: 33
  outliers final: 25
  residues processed: 170
  average time/residue: 0.2146
  time to fit residues: 52.0651
Evaluate side-chains
  164 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  116 ASP
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 60 optimal weight:    0.0010
   chunk 55 optimal weight:    0.0010
   chunk 5 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 63 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
A 331 GLN
** A 559 HIS ** 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 = 0.4107 r_free = 0.4107 target = 0.156081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.125509 restraints weight = 17808.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.128565 restraints weight = 11379.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.130577 restraints weight = 8622.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10415  Z= 0.161
  Angle     :  0.564   8.642  14058  Z= 0.282
  Chirality :  0.039   0.161   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.212  33.567   1398
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.08 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.33 (0.24), residues: 1274
  helix:  1.11 (0.20), residues: 722
  sheet: -2.03 (0.62), residues: 66
  loop : -2.03 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 119 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.008   0.001   PHE A 347 
 TYR   0.028   0.001   TYR E  28 
 ARG   0.003   0.000   ARG A 359 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8636 (ptm160)
REVERT: A  240 TRP cc_start: 0.5522 (m-10) cc_final: 0.4457 (p90)
REVERT: A  291 ARG cc_start: 0.6485 (ttt180) cc_final: 0.6179 (tpt-90)
REVERT: B  173 ASN cc_start: 0.8285 (m-40) cc_final: 0.7912 (t0)
REVERT: B  265 MET cc_start: 0.8468 (tpp) cc_final: 0.8108 (tpt)
REVERT: D   66 ILE cc_start: 0.8861 (pt) cc_final: 0.8251 (mt)
REVERT: E   14 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8304 (mtpp)
REVERT: E   16 MET cc_start: 0.7930 (tpt) cc_final: 0.7503 (tpt)
REVERT: E   27 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: E   51 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: E   55 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7732 (mt-10)
REVERT: E   56 TYR cc_start: 0.7914 (t80) cc_final: 0.7525 (t80)
REVERT: E   62 PHE cc_start: 0.7410 (m-80) cc_final: 0.6845 (m-80)
REVERT: E   63 LYS cc_start: 0.8733 (tttt) cc_final: 0.7867 (tptt)
REVERT: E   75 GLU cc_start: 0.8072 (pm20) cc_final: 0.7687 (mm-30)
  outliers start: 30
  outliers final: 25
  residues processed: 167
  average time/residue: 0.2177
  time to fit residues: 52.4904
Evaluate side-chains
  167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 41 optimal weight:    0.4980
   chunk 126 optimal weight:    8.9990
   chunk 93 optimal weight:    0.4980
   chunk 105 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN
C  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.152413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.124322 restraints weight = 17805.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.125335 restraints weight = 12713.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125353 restraints weight = 10501.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10415  Z= 0.273
  Angle     :  0.614   8.452  14058  Z= 0.307
  Chirality :  0.041   0.165   1581
  Planarity :  0.004   0.036   1809
  Dihedral  :  4.323  29.997   1398
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.81 %
    Favored  : 78.04 %
  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: -0.44 (0.24), residues: 1274
  helix:  1.00 (0.20), residues: 721
  sheet: -2.00 (0.62), residues: 66
  loop : -2.06 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 159 
 HIS   0.006   0.001   HIS A 559 
 PHE   0.012   0.001   PHE C 160 
 TYR   0.019   0.002   TYR D  83 
 ARG   0.003   0.000   ARG C  25 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 1.099 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8700 (ptm160)
REVERT: A  240 TRP cc_start: 0.5525 (m-10) cc_final: 0.4395 (p90)
REVERT: A  291 ARG cc_start: 0.6601 (ttt180) cc_final: 0.6275 (tpt-90)
REVERT: B  173 ASN cc_start: 0.8321 (m-40) cc_final: 0.7902 (t0)
REVERT: B  265 MET cc_start: 0.8542 (tpp) cc_final: 0.8075 (tpt)
REVERT: D   66 ILE cc_start: 0.8923 (pt) cc_final: 0.8391 (mt)
REVERT: E   14 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8362 (mtpp)
REVERT: E   16 MET cc_start: 0.8000 (tpt) cc_final: 0.7548 (tpt)
REVERT: E   27 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: E   51 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: E   55 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7798 (mt-10)
REVERT: E   56 TYR cc_start: 0.8029 (t80) cc_final: 0.7542 (t80)
REVERT: E   62 PHE cc_start: 0.7597 (m-80) cc_final: 0.7083 (m-80)
REVERT: E   75 GLU cc_start: 0.8180 (pm20) cc_final: 0.7646 (mm-30)
  outliers start: 35
  outliers final: 28
  residues processed: 161
  average time/residue: 0.2287
  time to fit residues: 52.1151
Evaluate side-chains
  160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9980
   chunk 111 optimal weight:    7.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN
C  57 GLN
C 144 GLN
** D  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.150366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.121262 restraints weight = 17898.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.123209 restraints weight = 12568.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.124080 restraints weight = 9959.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10415  Z= 0.329
  Angle     :  0.655   8.426  14058  Z= 0.327
  Chirality :  0.042   0.163   1581
  Planarity :  0.004   0.035   1809
  Dihedral  :  4.494  29.020   1398
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.90 %
    Favored  : 77.68 %
  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: -0.57 (0.24), residues: 1274
  helix:  0.84 (0.19), residues: 722
  sheet: -2.01 (0.61), residues: 66
  loop : -2.04 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 159 
 HIS   0.007   0.001   HIS A 559 
 PHE   0.015   0.002   PHE C 160 
 TYR   0.020   0.002   TYR D  83 
 ARG   0.004   0.000   ARG C  25 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8689 (ptm160)
REVERT: A  184 ASP cc_start: 0.7893 (m-30) cc_final: 0.7634 (m-30)
REVERT: A  240 TRP cc_start: 0.5549 (m-10) cc_final: 0.4353 (p90)
REVERT: A  291 ARG cc_start: 0.6681 (ttt180) cc_final: 0.6308 (tpt-90)
REVERT: B  173 ASN cc_start: 0.8367 (m-40) cc_final: 0.7915 (t0)
REVERT: B  265 MET cc_start: 0.8535 (tpp) cc_final: 0.8078 (tpt)
REVERT: D   66 ILE cc_start: 0.8920 (pt) cc_final: 0.8412 (mt)
REVERT: E   14 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8292 (mtpp)
REVERT: E   16 MET cc_start: 0.8091 (tpt) cc_final: 0.7513 (tpp)
REVERT: E   27 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7560 (tm-30)
REVERT: E   56 TYR cc_start: 0.8077 (t80) cc_final: 0.7518 (t80)
REVERT: E   62 PHE cc_start: 0.7652 (m-80) cc_final: 0.7084 (m-80)
REVERT: E   75 GLU cc_start: 0.8186 (pm20) cc_final: 0.7664 (mm-30)
  outliers start: 38
  outliers final: 29
  residues processed: 158
  average time/residue: 0.2247
  time to fit residues: 51.2401
Evaluate side-chains
  157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  261 ILE
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 119 optimal weight:    0.0040
   chunk 91 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
C  57 GLN
** D  73 HIS ** 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 = 0.4082 r_free = 0.4082 target = 0.153953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.124683 restraints weight = 17788.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.125982 restraints weight = 12085.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.126578 restraints weight = 8919.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10415  Z= 0.196
  Angle     :  0.595   8.337  14058  Z= 0.297
  Chirality :  0.040   0.174   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.335  32.586   1398
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.35 %
    Favored  : 78.13 %
  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: -0.31 (0.24), residues: 1274
  helix:  1.08 (0.20), residues: 721
  sheet: -2.00 (0.60), residues: 66
  loop : -1.95 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 138 
 HIS   0.006   0.001   HIS A 559 
 PHE   0.011   0.001   PHE A 275 
 TYR   0.024   0.001   TYR A 257 
 ARG   0.002   0.000   ARG A 112 

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 1.188 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8536 (ptm160)
REVERT: A  240 TRP cc_start: 0.5505 (m-10) cc_final: 0.4372 (p90)
REVERT: A  291 ARG cc_start: 0.6550 (ttt180) cc_final: 0.6238 (tpt-90)
REVERT: B  173 ASN cc_start: 0.8274 (m-40) cc_final: 0.7906 (t0)
REVERT: B  265 MET cc_start: 0.8470 (tpp) cc_final: 0.8186 (tpt)
REVERT: B  318 TYR cc_start: 0.8163 (m-10) cc_final: 0.7919 (m-10)
REVERT: D   66 ILE cc_start: 0.8908 (pt) cc_final: 0.8311 (mt)
REVERT: E   16 MET cc_start: 0.7859 (tpt) cc_final: 0.7336 (tpp)
REVERT: E   27 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7415 (tm-30)
REVERT: E   51 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: E   56 TYR cc_start: 0.7978 (t80) cc_final: 0.7414 (t80)
REVERT: E   62 PHE cc_start: 0.7561 (m-80) cc_final: 0.7050 (m-80)
REVERT: E   75 GLU cc_start: 0.8203 (pm20) cc_final: 0.7703 (mm-30)
  outliers start: 28
  outliers final: 24
  residues processed: 153
  average time/residue: 0.2158
  time to fit residues: 47.7380
Evaluate side-chains
  151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0970
   chunk 0 optimal weight:    8.9990
   chunk 84 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN
** D  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.153741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.124797 restraints weight = 17568.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.126643 restraints weight = 11667.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.127939 restraints weight = 8668.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10415  Z= 0.193
  Angle     :  0.599   8.381  14058  Z= 0.300
  Chirality :  0.040   0.185   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.283  32.511   1398
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.53 %
    Favored  : 77.68 %
  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: -0.22 (0.24), residues: 1274
  helix:  1.15 (0.20), residues: 719
  sheet: -2.02 (0.59), residues: 66
  loop : -1.89 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 119 
 HIS   0.006   0.001   HIS A 559 
 PHE   0.010   0.001   PHE C 160 
 TYR   0.021   0.001   TYR A 257 
 ARG   0.003   0.000   ARG A 375 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2956.97 seconds
wall clock time: 54 minutes 13.29 seconds (3253.29 seconds total)