Starting phenix.real_space_refine
on Mon Jul 28 08:52:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sz9_10350/07_2025/6sz9_10350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sz9_10350/07_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_10350/07_2025/6sz9_10350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sz9_10350/07_2025/6sz9_10350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sz9_10350/07_2025/6sz9_10350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sz9_10350/07_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-5711/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: 7.11, per 1000 atoms: 0.69
  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: 3.18
  Conformation dependent library (CDL) restraints added in 1.1 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: 2.84

  Time building geometry restraints manager: 2.84 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:             3.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.860
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.600
-------------------------------------------------------------------------------
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   0.160  10419  Z= 0.237
  Angle     :  0.868  26.533  14064  Z= 0.462
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11761 (  521)
  hydrogen bonds       : angle       6.15066 ( 1542)
  metal coordination   : bond        0.11764 (    4)
  metal coordination   : angle      14.13546 (    6)
  covalent geometry    : bond        0.00452 (10415)
  covalent geometry    : angle       0.81718 (14058)

*********************** 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  : 1.236 
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: 0.2484
  time to fit residues: 70.9384
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  : 1.161 
-------------------------------------------------------------------------------
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 = 17494.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.128059 restraints weight = 11103.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130119 restraints weight = 8384.240|
|-----------------------------------------------------------------------------|
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  10419  Z= 0.133
  Angle     :  0.590   9.332  14064  Z= 0.303
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04717 (  521)
  hydrogen bonds       : angle       4.60667 ( 1542)
  metal coordination   : bond        0.01014 (    4)
  metal coordination   : angle       4.95587 (    6)
  covalent geometry    : bond        0.00291 (10415)
  covalent geometry    : angle       0.58134 (14058)

*********************** 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  : 1.178 
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: 0.7482 (mmp)
REVERT: A  405 MET cc_start: 0.7074 (mtp) cc_final: 0.6771 (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: 0.7132 (mt) cc_final: 0.6884 (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: 0.8608 (mm)
REVERT: E   14 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8215 (mtpp)
REVERT: E   16 MET cc_start: 0.7796 (mmm) cc_final: 0.7584 (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: 0.8112 (tm-30)
REVERT: E   56 TYR cc_start: 0.7676 (t80) cc_final: 0.7469 (t80)
REVERT: E   62 PHE cc_start: 0.7165 (m-80) cc_final: 0.6698 (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: 0.2307
  time to fit residues: 55.9321
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  : 1.101 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 113 optimal weight:    0.8980
   chunk 109 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 253 GLN
D 277 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.154662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.123849 restraints weight = 17726.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126943 restraints weight = 11466.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.128928 restraints weight = 8736.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10419  Z= 0.138
  Angle     :  0.568  10.280  14064  Z= 0.289
  Chirality :  0.039   0.169   1581
  Planarity :  0.004   0.042   1809
  Dihedral  :  4.555  33.806   1400
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.29 %
    Favored  : 81.73 %
  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: -1.15 (0.23), residues: 1274
  helix:  0.36 (0.20), residues: 718
  sheet: -1.88 (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   0.013   0.001   PHE C 179 
 TYR   0.009   0.001   TYR D  83 
 ARG   0.007   0.000   ARG E  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04409 (  521)
  hydrogen bonds       : angle       4.33768 ( 1542)
  metal coordination   : bond        0.00732 (    4)
  metal coordination   : angle       4.27738 (    6)
  covalent geometry    : bond        0.00315 (10415)
  covalent geometry    : angle       0.56135 (14058)

*********************** 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
  172 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5537 (m-10) cc_final: 0.4615 (p90)
REVERT: A  405 MET cc_start: 0.6953 (mtp) cc_final: 0.6615 (mtp)
REVERT: B  173 ASN cc_start: 0.8278 (m-40) cc_final: 0.7854 (t0)
REVERT: C   62 LEU cc_start: 0.7166 (mt) cc_final: 0.6964 (mt)
REVERT: D   66 ILE cc_start: 0.8871 (pt) cc_final: 0.8275 (mt)
REVERT: D  116 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7544 (t0)
REVERT: E   14 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8256 (mtpp)
REVERT: E   27 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: E   55 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7794 (mt-10)
REVERT: E   62 PHE cc_start: 0.7327 (m-80) cc_final: 0.6766 (m-80)
REVERT: E   63 LYS cc_start: 0.8358 (ttpp) cc_final: 0.7662 (tptt)
REVERT: E   75 GLU cc_start: 0.8088 (pm20) cc_final: 0.7613 (mm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 163
  average time/residue: 0.2431
  time to fit residues: 55.0575
Evaluate side-chains
  157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
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  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 C residue   84 CYS
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:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 109 optimal weight:    0.0020
   chunk 56 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 114 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.4188

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.156657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.126297 restraints weight = 17544.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.129399 restraints weight = 11269.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.131426 restraints weight = 8548.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10419  Z= 0.113
  Angle     :  0.537   8.962  14064  Z= 0.273
  Chirality :  0.039   0.174   1581
  Planarity :  0.003   0.035   1809
  Dihedral  :  4.352  35.074   1398
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.47 %
    Favored  : 80.83 %
  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: -0.76 (0.23), residues: 1274
  helix:  0.75 (0.20), residues: 715
  sheet: -2.27 (0.61), residues: 66
  loop : -2.16 (0.25), residues: 493

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   0.008   0.001   TYR A 257 
 ARG   0.011   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  521)
  hydrogen bonds       : angle       4.14300 ( 1542)
  metal coordination   : bond        0.00376 (    4)
  metal coordination   : angle       3.64146 (    6)
  covalent geometry    : bond        0.00247 (10415)
  covalent geometry    : angle       0.53202 (14058)

*********************** 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: 30
    poor density    : 159
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5555 (m-10) cc_final: 0.4643 (p90)
REVERT: A  405 MET cc_start: 0.6733 (mtp) cc_final: 0.6480 (mtp)
REVERT: B  173 ASN cc_start: 0.8271 (m-40) cc_final: 0.7835 (t0)
REVERT: B  189 GLU cc_start: 0.7586 (tt0) cc_final: 0.7254 (tt0)
REVERT: B  265 MET cc_start: 0.8417 (tpp) cc_final: 0.8112 (tpt)
REVERT: B  318 TYR cc_start: 0.8013 (m-10) cc_final: 0.7759 (m-10)
REVERT: D   66 ILE cc_start: 0.8888 (pt) cc_final: 0.8249 (mt)
REVERT: E   14 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8262 (mtpp)
REVERT: E   16 MET cc_start: 0.7865 (tpt) cc_final: 0.7436 (tpt)
REVERT: E   27 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7469 (tm-30)
REVERT: E   51 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: E   55 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7951 (mt-10)
REVERT: E   56 TYR cc_start: 0.8008 (t80) cc_final: 0.7625 (t80)
REVERT: E   62 PHE cc_start: 0.7368 (m-80) cc_final: 0.6819 (m-80)
REVERT: E   75 GLU cc_start: 0.8039 (pm20) cc_final: 0.7595 (mm-30)
  outliers start: 30
  outliers final: 18
  residues processed: 180
  average time/residue: 0.2151
  time to fit residues: 55.7880
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  : 1.165 
-------------------------------------------------------------------------------
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  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  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:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 78 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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
B 133 GLN
B 326 GLN
C  36 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.152064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.122448 restraints weight = 17672.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.124948 restraints weight = 12336.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126576 restraints weight = 9812.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10419  Z= 0.182
  Angle     :  0.614   8.959  14064  Z= 0.307
  Chirality :  0.041   0.161   1581
  Planarity :  0.004   0.040   1809
  Dihedral  :  4.430  30.810   1398
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.19 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.23), residues: 1274
  helix:  0.76 (0.20), residues: 714
  sheet: -2.08 (0.62), residues: 66
  loop : -2.13 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 308 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.012   0.001   PHE B 168 
 TYR   0.013   0.001   TYR D  83 
 ARG   0.007   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04534 (  521)
  hydrogen bonds       : angle       4.31856 ( 1542)
  metal coordination   : bond        0.01042 (    4)
  metal coordination   : angle       4.30541 (    6)
  covalent geometry    : bond        0.00429 (10415)
  covalent geometry    : angle       0.60737 (14058)

*********************** 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
  177 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5533 (m-10) cc_final: 0.4507 (p90)
REVERT: A  291 ARG cc_start: 0.6517 (ttt180) cc_final: 0.6222 (tpt-90)
REVERT: A  405 MET cc_start: 0.6834 (mtp) cc_final: 0.6532 (mtp)
REVERT: B  173 ASN cc_start: 0.8304 (m-40) cc_final: 0.7918 (t0)
REVERT: B  265 MET cc_start: 0.8476 (tpp) cc_final: 0.8092 (tpt)
REVERT: D   66 ILE cc_start: 0.8896 (pt) cc_final: 0.8364 (mt)
REVERT: D  116 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7601 (t0)
REVERT: E   14 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8351 (mtpp)
REVERT: E   16 MET cc_start: 0.8023 (tpt) cc_final: 0.7526 (tpt)
REVERT: E   27 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: E   51 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8243 (tm-30)
REVERT: E   55 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: E   56 TYR cc_start: 0.8091 (t80) cc_final: 0.7660 (t80)
REVERT: E   62 PHE cc_start: 0.7461 (m-80) cc_final: 0.6974 (m-80)
REVERT: E   63 LYS cc_start: 0.8699 (tttt) cc_final: 0.7805 (tptt)
REVERT: E   75 GLU cc_start: 0.8085 (pm20) cc_final: 0.7634 (mm-30)
  outliers start: 34
  outliers final: 24
  residues processed: 168
  average time/residue: 0.2073
  time to fit residues: 50.1702
Evaluate side-chains
  164 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
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  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  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   31 ILE
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  225 ILE
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:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 109 optimal weight:    9.9990
   chunk 120 optimal weight:    0.0980
   chunk 77 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   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
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.154329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.123738 restraints weight = 17564.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.126687 restraints weight = 11376.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.128655 restraints weight = 8707.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10419  Z= 0.126
  Angle     :  0.571   8.617  14064  Z= 0.285
  Chirality :  0.039   0.159   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.319  33.176   1398
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.82 %
    Favored  : 79.12 %
  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: -0.47 (0.24), residues: 1274
  helix:  0.98 (0.20), residues: 714
  sheet: -2.06 (0.62), residues: 66
  loop : -2.05 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 308 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.008   0.001   PHE C 179 
 TYR   0.015   0.001   TYR D  83 
 ARG   0.005   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  521)
  hydrogen bonds       : angle       4.16210 ( 1542)
  metal coordination   : bond        0.00478 (    4)
  metal coordination   : angle       3.49473 (    6)
  covalent geometry    : bond        0.00285 (10415)
  covalent geometry    : angle       0.56694 (14058)

*********************** 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
  181 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 1.167 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8633 (ptm160)
REVERT: A  240 TRP cc_start: 0.5556 (m-10) cc_final: 0.4482 (p90)
REVERT: A  291 ARG cc_start: 0.6503 (ttt180) cc_final: 0.6198 (tpt-90)
REVERT: A  405 MET cc_start: 0.6752 (mtp) cc_final: 0.6456 (mtp)
REVERT: B  173 ASN cc_start: 0.8287 (m-40) cc_final: 0.7907 (t0)
REVERT: B  265 MET cc_start: 0.8436 (tpp) cc_final: 0.8071 (tpt)
REVERT: B  318 TYR cc_start: 0.8078 (m-10) cc_final: 0.7726 (m-10)
REVERT: D   66 ILE cc_start: 0.8897 (pt) cc_final: 0.8276 (mt)
REVERT: E   14 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8331 (mtpp)
REVERT: E   16 MET cc_start: 0.7968 (tpt) cc_final: 0.7532 (tpt)
REVERT: E   27 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: E   51 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8209 (tm-30)
REVERT: E   55 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: E   56 TYR cc_start: 0.8049 (t80) cc_final: 0.7499 (t80)
REVERT: E   62 PHE cc_start: 0.7402 (m-80) cc_final: 0.6936 (m-80)
REVERT: E   63 LYS cc_start: 0.8699 (tttt) cc_final: 0.7861 (tptt)
REVERT: E   75 GLU cc_start: 0.8064 (pm20) cc_final: 0.7679 (mm-30)
  outliers start: 34
  outliers final: 26
  residues processed: 172
  average time/residue: 0.2213
  time to fit residues: 54.1899
Evaluate side-chains
  165 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
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  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  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   12 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:    0.3980
   chunk 55 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 112 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 110 optimal weight:    0.3980
   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
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.154922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.124105 restraints weight = 17814.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.127144 restraints weight = 11437.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129094 restraints weight = 8696.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10419  Z= 0.126
  Angle     :  0.574   8.081  14064  Z= 0.284
  Chirality :  0.039   0.158   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.257  32.837   1398
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.27 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.24), residues: 1274
  helix:  1.04 (0.20), residues: 722
  sheet: -2.13 (0.61), residues: 66
  loop : -2.07 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 308 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.010   0.001   PHE A 347 
 TYR   0.016   0.001   TYR D  83 
 ARG   0.005   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  521)
  hydrogen bonds       : angle       4.10465 ( 1542)
  metal coordination   : bond        0.00471 (    4)
  metal coordination   : angle       3.35040 (    6)
  covalent geometry    : bond        0.00287 (10415)
  covalent geometry    : angle       0.56980 (14058)

*********************** 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: 33
    poor density    : 144
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8654 (ptm160)
REVERT: A  240 TRP cc_start: 0.5499 (m-10) cc_final: 0.4426 (p90)
REVERT: A  291 ARG cc_start: 0.6491 (ttt180) cc_final: 0.6188 (tpt-90)
REVERT: A  405 MET cc_start: 0.6659 (mtp) cc_final: 0.6419 (mtp)
REVERT: B  173 ASN cc_start: 0.8283 (m-40) cc_final: 0.7902 (t0)
REVERT: B  189 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7142 (tt0)
REVERT: B  265 MET cc_start: 0.8446 (tpp) cc_final: 0.8084 (tpt)
REVERT: B  318 TYR cc_start: 0.8098 (m-10) cc_final: 0.7843 (m-10)
REVERT: D   66 ILE cc_start: 0.8904 (pt) cc_final: 0.8299 (mt)
REVERT: E   14 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8336 (mtpp)
REVERT: E   16 MET cc_start: 0.8031 (tpt) cc_final: 0.7599 (tpt)
REVERT: E   27 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7518 (tm-30)
REVERT: E   51 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: E   55 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: E   56 TYR cc_start: 0.7996 (t80) cc_final: 0.7447 (t80)
REVERT: E   62 PHE cc_start: 0.7457 (m-80) cc_final: 0.6989 (m-80)
REVERT: E   63 LYS cc_start: 0.8723 (tttt) cc_final: 0.7854 (tptt)
REVERT: E   75 GLU cc_start: 0.8095 (pm20) cc_final: 0.7671 (mm-30)
  outliers start: 33
  outliers final: 27
  residues processed: 167
  average time/residue: 0.2218
  time to fit residues: 52.9177
Evaluate side-chains
  166 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
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  189 GLU
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  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
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   12 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 123 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 331 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.151098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.122515 restraints weight = 17830.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.123709 restraints weight = 12770.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.124709 restraints weight = 10744.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10419  Z= 0.196
  Angle     :  0.634   8.212  14064  Z= 0.315
  Chirality :  0.041   0.158   1581
  Planarity :  0.004   0.036   1809
  Dihedral  :  4.407  29.615   1398
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.45 %
    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: -0.54 (0.24), residues: 1274
  helix:  0.89 (0.20), residues: 722
  sheet: -2.05 (0.62), residues: 66
  loop : -2.07 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 159 
 HIS   0.006   0.001   HIS A 559 
 PHE   0.012   0.001   PHE C 160 
 TYR   0.018   0.002   TYR D  83 
 ARG   0.005   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04618 (  521)
  hydrogen bonds       : angle       4.30036 ( 1542)
  metal coordination   : bond        0.01067 (    4)
  metal coordination   : angle       3.80057 (    6)
  covalent geometry    : bond        0.00466 (10415)
  covalent geometry    : angle       0.62880 (14058)

*********************** 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
  172 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8665 (ptm160)
REVERT: A  240 TRP cc_start: 0.5445 (m-10) cc_final: 0.4339 (p90)
REVERT: A  291 ARG cc_start: 0.6577 (ttt180) cc_final: 0.6248 (tpt-90)
REVERT: A  405 MET cc_start: 0.6813 (mtp) cc_final: 0.6432 (mtp)
REVERT: B  173 ASN cc_start: 0.8335 (m-40) cc_final: 0.7900 (t0)
REVERT: B  265 MET cc_start: 0.8525 (tpp) cc_final: 0.8065 (tpt)
REVERT: D   66 ILE cc_start: 0.8936 (pt) cc_final: 0.8411 (mt)
REVERT: E   14 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8273 (mtpp)
REVERT: E   16 MET cc_start: 0.8000 (tpt) cc_final: 0.7609 (tpt)
REVERT: E   27 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7496 (tm-30)
REVERT: E   51 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8199 (tm-30)
REVERT: E   55 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: E   56 TYR cc_start: 0.8062 (t80) cc_final: 0.7532 (t80)
REVERT: E   62 PHE cc_start: 0.7538 (m-80) cc_final: 0.7024 (m-80)
REVERT: E   63 LYS cc_start: 0.8801 (tttt) cc_final: 0.7878 (tptt)
REVERT: E   75 GLU cc_start: 0.8154 (pm20) cc_final: 0.7642 (mm-30)
  outliers start: 39
  outliers final: 33
  residues processed: 162
  average time/residue: 0.2190
  time to fit residues: 51.2306
Evaluate side-chains
  162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
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  286 THR
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  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue   38 ILE
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   12 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
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   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:    0.5980
   chunk 27 optimal weight:    7.9990
   chunk 99 optimal weight:    0.7980
   chunk 111 optimal weight:    8.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN
C  36 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 = 0.4065 r_free = 0.4065 target = 0.152549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.123649 restraints weight = 17771.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.124681 restraints weight = 12811.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.126096 restraints weight = 10910.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10419  Z= 0.156
  Angle     :  0.602   7.842  14064  Z= 0.299
  Chirality :  0.040   0.162   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.353  31.459   1398
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.81 %
    Favored  : 77.95 %
  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: -0.43 (0.24), residues: 1274
  helix:  1.00 (0.20), residues: 721
  sheet: -2.01 (0.61), residues: 66
  loop : -2.04 (0.27), residues: 487

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   0.011   0.001   PHE C 160 
 TYR   0.019   0.001   TYR D  83 
 ARG   0.005   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  521)
  hydrogen bonds       : angle       4.21686 ( 1542)
  metal coordination   : bond        0.00727 (    4)
  metal coordination   : angle       3.39344 (    6)
  covalent geometry    : bond        0.00364 (10415)
  covalent geometry    : angle       0.59760 (14058)

*********************** 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: 36
    poor density    : 132
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8700 (ptm160)
REVERT: A  240 TRP cc_start: 0.5483 (m-10) cc_final: 0.4336 (p90)
REVERT: A  291 ARG cc_start: 0.6605 (ttt180) cc_final: 0.6262 (tpt-90)
REVERT: A  405 MET cc_start: 0.6848 (mtp) cc_final: 0.6506 (mtp)
REVERT: B  173 ASN cc_start: 0.8325 (m-40) cc_final: 0.7894 (t0)
REVERT: B  265 MET cc_start: 0.8502 (tpp) cc_final: 0.8144 (tpt)
REVERT: D   66 ILE cc_start: 0.8921 (pt) cc_final: 0.8367 (mt)
REVERT: E   14 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8304 (mtpp)
REVERT: E   16 MET cc_start: 0.8062 (tpt) cc_final: 0.7699 (tpt)
REVERT: E   27 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7462 (tm-30)
REVERT: E   51 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8315 (tm-30)
REVERT: E   55 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: E   56 TYR cc_start: 0.8111 (t80) cc_final: 0.7513 (t80)
REVERT: E   62 PHE cc_start: 0.7645 (m-80) cc_final: 0.7075 (m-80)
REVERT: E   75 GLU cc_start: 0.8167 (pm20) cc_final: 0.7635 (mm-30)
  outliers start: 36
  outliers final: 30
  residues processed: 158
  average time/residue: 0.2092
  time to fit residues: 47.8089
Evaluate side-chains
  161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
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  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  371 THR
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  261 ILE
Chi-restraints excluded: chain E residue   12 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
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:    1.9990
   chunk 32 optimal weight:    0.0170
   chunk 29 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0070
   chunk 91 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.155064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.126677 restraints weight = 17769.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.128006 restraints weight = 12842.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.129412 restraints weight = 10079.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10419  Z= 0.118
  Angle     :  0.573   8.294  14064  Z= 0.285
  Chirality :  0.039   0.166   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.213  33.847   1398
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.62 %
    Favored  : 77.86 %
  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: 723
  sheet: -1.99 (0.60), residues: 66
  loop : -1.91 (0.27), residues: 485

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   0.011   0.001   PHE A 275 
 TYR   0.017   0.001   TYR D  83 
 ARG   0.005   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  521)
  hydrogen bonds       : angle       4.06663 ( 1542)
  metal coordination   : bond        0.00321 (    4)
  metal coordination   : angle       3.10625 (    6)
  covalent geometry    : bond        0.00264 (10415)
  covalent geometry    : angle       0.56995 (14058)

********************** 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
  167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8680 (ptm160)
REVERT: A  240 TRP cc_start: 0.5674 (m-10) cc_final: 0.4473 (p90)
REVERT: A  291 ARG cc_start: 0.6545 (ttt180) cc_final: 0.6192 (tpt-90)
REVERT: A  405 MET cc_start: 0.6663 (mtp) cc_final: 0.6364 (mtp)
REVERT: B  173 ASN cc_start: 0.8308 (m-40) cc_final: 0.7893 (t0)
REVERT: B  265 MET cc_start: 0.8468 (tpp) cc_final: 0.8186 (tpt)
REVERT: B  318 TYR cc_start: 0.7936 (m-10) cc_final: 0.7689 (m-10)
REVERT: D   66 ILE cc_start: 0.8869 (pt) cc_final: 0.8269 (mt)
REVERT: E   14 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8168 (mtpp)
REVERT: E   16 MET cc_start: 0.8066 (tpt) cc_final: 0.7762 (tpt)
REVERT: E   27 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7318 (tm-30)
REVERT: E   51 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8299 (tm-30)
REVERT: E   55 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8083 (mt-10)
REVERT: E   56 TYR cc_start: 0.8031 (t80) cc_final: 0.7562 (t80)
REVERT: E   62 PHE cc_start: 0.7655 (m-80) cc_final: 0.7108 (m-80)
REVERT: E   75 GLU cc_start: 0.8161 (pm20) cc_final: 0.7691 (mm-30)
  outliers start: 28
  outliers final: 25
  residues processed: 160
  average time/residue: 0.2151
  time to fit residues: 49.6972
Evaluate side-chains
  156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
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  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  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 E residue   12 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:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0370
   chunk 0 optimal weight:    8.9990
   chunk 84 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.2662

-------------------------------------------------------------------------------
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 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN
C  36 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 = 0.4065 r_free = 0.4065 target = 0.152463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123987 restraints weight = 17602.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.125379 restraints weight = 12504.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.126797 restraints weight = 10070.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10419  Z= 0.168
  Angle     :  0.622   8.335  14064  Z= 0.310
  Chirality :  0.041   0.165   1581
  Planarity :  0.003   0.035   1809
  Dihedral  :  4.296  30.897   1398
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.62 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.24), residues: 1274
  helix:  1.11 (0.20), residues: 721
  sheet: -1.97 (0.61), residues: 66
  loop : -1.93 (0.27), residues: 487

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   0.012   0.001   PHE C 160 
 TYR   0.020   0.001   TYR D  83 
 ARG   0.005   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  521)
  hydrogen bonds       : angle       4.20227 ( 1542)
  metal coordination   : bond        0.00819 (    4)
  metal coordination   : angle       3.59439 (    6)
  covalent geometry    : bond        0.00400 (10415)
  covalent geometry    : angle       0.61728 (14058)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3283.23 seconds
wall clock time: 57 minutes 50.98 seconds (3470.98 seconds total)