Starting phenix.real_space_refine
on Fri Jul  3 15:16:42 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8g3f_29694/07_2026/8g3f_29694.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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
     P       2      5.49       5
     S      62      5.16       5
     C    9385      2.51       5
     N    2374      2.21       5
     O    2619      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14442
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5000
          Classifications: {'peptide': 635}
          Link IDs: {'PTRANS': 10, 'TRANS': 624}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1915
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 5, 'TRANS': 238}
    Chain: "C"
      Number of atoms: 1915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1915
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 5, 'TRANS': 238}
    Chain: "D"
      Number of atoms: 2738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2738
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 324}
    Chain: "E"
      Number of atoms: 2738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2738
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 116
          Unusual residues: {'6OU': 2, 'PLM': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'OLA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.39, per 1000 atoms: 0.23
  Number of scatterers: 14442
  At special positions: 0
  Unit cell: (95.048, 113.36, 198.816, 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)
     S      62     16.00
     P       2     15.00
     O    2619      8.00
     N    2374      7.00
     C    9385      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 635.0 milliseconds
  

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3374

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 12 sheets defined
      61.9% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 18
    Processing helix  chain 'A' and resid 19 through 40
      removed outlier: 3.640A  pdb=" N   TYR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 47
      removed outlier: 3.836A  pdb=" N   ASN A  45 " --> pdb=" O   PRO A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 80
      removed outlier: 3.621A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A  80 " --> pdb=" O   ASN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 94
      removed outlier: 3.586A  pdb=" N   ILE A  87 " --> pdb=" O   ARG A  83 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU A  89 " --> pdb=" O   LYS A  85 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLY A  94 " --> pdb=" O   PHE A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 104
      removed outlier: 3.839A  pdb=" N   ILE A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   PHE A 101 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ARG A 102 " --> pdb=" O   HIS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 122
    Processing helix  chain 'A' and resid 126 through 138
      removed outlier: 3.560A  pdb=" N   LYS A 136 " --> pdb=" O   MET A 132 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 176
      removed outlier: 4.291A  pdb=" N   VAL A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN A 155 " --> pdb=" O   GLN A 151 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LYS A 176 " --> pdb=" O   TYR A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 222
      removed outlier: 4.371A  pdb=" N   GLY A 205 " --> pdb=" O   GLN A 201 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   ALA A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLU A 221 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 253
      removed outlier: 4.302A  pdb=" N   VAL A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 236 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   TYR A 252 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS A 253 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 265
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 3.614A  pdb=" N   SER A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   SER A 281 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.980A  pdb=" N   SER A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN A 289 " --> pdb=" O   ARG A 285 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 284 through 289'
    Processing helix  chain 'A' and resid 292 through 325
      removed outlier: 3.653A  pdb=" N   TYR A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   TYR A 315 " --> pdb=" O   TYR A 311 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLU A 318 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ALA A 321 " --> pdb=" O   SER A 317 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   VAL A 325 " --> pdb=" O   ALA A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 346
      removed outlier: 3.902A  pdb=" N   GLU A 346 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 382
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.776A  pdb=" N   GLN A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LYS A 414 " --> pdb=" O   ASP A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 472
      removed outlier: 3.601A  pdb=" N   GLN A 467 " --> pdb=" O   SER A 463 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS A 470 " --> pdb=" O   LYS A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 505
    Processing helix  chain 'A' and resid 515 through 556
      removed outlier: 4.031A  pdb=" N   ALA A 519 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   GLN A 520 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LYS A 521 " --> pdb=" O   SER A 517 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LYS A 549 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   GLN A 550 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   MET A 551 " --> pdb=" O   TYR A 547 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   GLY A 552 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 566
      removed outlier: 3.544A  pdb=" N   LYS A 566 " --> pdb=" O   THR A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 602
      removed outlier: 3.774A  pdb=" N   LYS A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE A 580 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   MET A 583 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ILE A 588 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      Proline residue:  A 589  - end of helix
      removed outlier: 3.514A  pdb=" N   GLN A 602 " --> pdb=" O   TYR A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 608
      removed outlier: 5.486A  pdb=" N   PHE A 606 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 607 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE A 608 " --> pdb=" O   TRP A 605 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 603 through 608'
    Processing helix  chain 'A' and resid 614 through 633
      removed outlier: 3.969A  pdb=" N   MET A 618 " --> pdb=" O   ALA A 614 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   PHE A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLY A 631 " --> pdb=" O   TYR A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 644
      removed outlier: 3.804A  pdb=" N   LYS A 640 " --> pdb=" O   LEU A 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 54
    Processing helix  chain 'B' and resid 75 through 86
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 107 through 111
    Processing helix  chain 'B' and resid 117 through 132
      removed outlier: 3.745A  pdb=" N   GLU B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 137
      removed outlier: 4.120A  pdb=" N   ARG B 137 " --> pdb=" O   TYR B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 144
      removed outlier: 3.603A  pdb=" N   ILE B 144 " --> pdb=" O   PRO B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 158
      removed outlier: 3.604A  pdb=" N   LYS B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLN B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 193
    Processing helix  chain 'B' and resid 203 through 209
      removed outlier: 4.091A  pdb=" N   TYR B 209 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 246
    Processing helix  chain 'C' and resid 45 through 55
    Processing helix  chain 'C' and resid 75 through 86
    Processing helix  chain 'C' and resid 101 through 108
      removed outlier: 3.526A  pdb=" N   ILE C 106 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 132
      removed outlier: 3.669A  pdb=" N   ALA C 120 " --> pdb=" O   SER C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 157
      removed outlier: 3.928A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 193
    Processing helix  chain 'C' and resid 203 through 209
      removed outlier: 3.998A  pdb=" N   TYR C 209 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 246
    Processing helix  chain 'D' and resid 2 through 9
    Processing helix  chain 'D' and resid 9 through 29
      removed outlier: 3.649A  pdb=" N   ILE D  13 " --> pdb=" O   ARG D   9 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA D  14 " --> pdb=" O   ARG D  10 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ALA D  15 " --> pdb=" O   SER D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 61
      removed outlier: 3.569A  pdb=" N   VAL D  38 " --> pdb=" O   SER D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 71
      removed outlier: 3.612A  pdb=" N   GLU D  71 " --> pdb=" O   LEU D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 139
      removed outlier: 4.381A  pdb=" N   VAL D  90 " --> pdb=" O   PHE D  86 " (cutoff:3.500A)
      Proline residue:  D 129  - end of helix
    Processing helix  chain 'D' and resid 142 through 169
    Processing helix  chain 'D' and resid 170 through 176
      removed outlier: 5.178A  pdb=" N   GLU D 173 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   LEU D 176 " --> pdb=" O   GLU D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 194
    Processing helix  chain 'D' and resid 194 through 202
    Processing helix  chain 'D' and resid 217 through 235
    Processing helix  chain 'D' and resid 264 through 271
      Proline residue:  D 269  - end of helix
    Processing helix  chain 'D' and resid 281 through 285
      removed outlier: 3.599A  pdb=" N   GLN D 285 " --> pdb=" O   HIS D 282 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 290 through 300
      removed outlier: 4.007A  pdb=" N   ALA D 300 " --> pdb=" O   LYS D 296 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 326 through 334
      removed outlier: 3.986A  pdb=" N   HIS D 330 " --> pdb=" O   ASN D 326 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL D 331 " --> pdb=" O   GLN D 327 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 9
    Processing helix  chain 'E' and resid 11 through 30
      removed outlier: 3.563A  pdb=" N   ASP E  30 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 34 through 37
      removed outlier: 3.592A  pdb=" N   ASN E  37 " --> pdb=" O   SER E  34 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 34 through 37'
    Processing helix  chain 'E' and resid 38 through 61
      removed outlier: 4.090A  pdb=" N   ARG E  58 " --> pdb=" O   TRP E  54 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LYS E  59 " --> pdb=" O   PHE E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 71
      removed outlier: 4.075A  pdb=" N   LYS E  68 " --> pdb=" O   TYR E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 79
      removed outlier: 4.180A  pdb=" N   ILE E  79 " --> pdb=" O   VAL E  76 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 138
      removed outlier: 3.654A  pdb=" N   ALA E  88 " --> pdb=" O   THR E  84 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   MET E  89 " --> pdb=" O   PRO E  85 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL E  90 " --> pdb=" O   PHE E  86 " (cutoff:3.500A)
      Proline residue:  E 129  - end of helix
    Processing helix  chain 'E' and resid 143 through 170
    Processing helix  chain 'E' and resid 171 through 175
    Processing helix  chain 'E' and resid 182 through 194
      removed outlier: 4.278A  pdb=" N   LEU E 186 " --> pdb=" O   GLN E 182 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 194 through 202
    Processing helix  chain 'E' and resid 218 through 235
    Processing helix  chain 'E' and resid 264 through 268
    Processing helix  chain 'E' and resid 281 through 287
      removed outlier: 3.748A  pdb=" N   ALA E 286 " --> pdb=" O   HIS E 283 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 289 through 300
      removed outlier: 4.551A  pdb=" N   TYR E 293 " --> pdb=" O   GLY E 289 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 324 through 327
    Processing helix  chain 'E' and resid 328 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330
      removed outlier: 3.602A  pdb=" N   LEU A 511 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 364
      removed outlier: 8.822A  pdb=" N   VAL A 458 " --> pdb=" O   GLN A 384 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ALA A 386 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ALA A 457 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 404 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   ALA A 403 " --> pdb=" O   TYR A 437 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   GLY A 439 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS A 425 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30
      removed outlier: 5.859A  pdb=" N   ALA B   6 " --> pdb=" O   HIS B  65 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   HIS B  65 " --> pdb=" O   ALA B   6 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LYS B   8 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   THR B  63 " --> pdb=" O   LYS B   8 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   HIS B  61 " --> pdb=" O   ARG B  10 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14
    Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 90
      removed outlier: 7.457A  pdb=" N   GLY B  88 " --> pdb=" O   PHE B 166 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ILE B 165 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   VAL B 200 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   ALA B 167 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   MET B 199 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   PHE B  35 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ILE B 214 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   SER B  37 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 29
      removed outlier: 4.024A  pdb=" N   GLU C   5 " --> pdb=" O   HIS C  65 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   HIS C  65 " --> pdb=" O   GLU C   5 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 39
    Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88
      removed outlier: 6.568A  pdb=" N   GLY C  88 " --> pdb=" O   PHE C 166 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE C 198 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 179 through 182
    Processing sheet with id=AB1, first strand: chain 'D' and resid 205 through 209
      removed outlier: 3.611A  pdb=" N   ILE D 243 " --> pdb=" O   ASP D 206 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER D 245 " --> pdb=" O   GLN D 208 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 179 through 181
      removed outlier: 3.725A  pdb=" N   GLU E 179 " --> pdb=" O   SER E 216 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER E 216 " --> pdb=" O   GLU E 179 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209
      removed outlier: 3.567A  pdb=" N   GLN E 208 " --> pdb=" O   ILE E 243 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER E 245 " --> pdb=" O   GLN E 208 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU E 320 " --> pdb=" O   LEU E 254 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   HIS E 305 " --> pdb=" O   THR E 321 " (cutoff:3.500A)

    793 hydrogen bonds defined for protein.
    2268 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: 2.54

  Time building geometry restraints manager: 1.63 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.32: 2343
        1.32 -     1.44: 3765
        1.44 -     1.57: 8465
        1.57 -     1.69: 22
        1.69 -     1.82: 114
  Bond restraints: 14709
  Sorted by residual:
  bond pdb=" C10 OLA E 401 "
       pdb=" C9  OLA E 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.469 -0.137 2.00e-02 2.50e+03 4.71e+01
  bond pdb=" C16 6OU A 702 "
       pdb=" O18 6OU A 702 "
    ideal  model  delta    sigma   weight residual
    1.327  1.464 -0.137 2.00e-02 2.50e+03 4.66e+01
  bond pdb=" C16 6OU A 703 "
       pdb=" O18 6OU A 703 "
    ideal  model  delta    sigma   weight residual
    1.327  1.462 -0.135 2.00e-02 2.50e+03 4.57e+01
  bond pdb=" C31 6OU A 703 "
       pdb=" O30 6OU A 703 "
    ideal  model  delta    sigma   weight residual
    1.331  1.424 -0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C14 6OU A 702 "
       pdb=" C15 6OU A 702 "
    ideal  model  delta    sigma   weight residual
    1.521  1.609 -0.088 2.00e-02 2.50e+03 1.95e+01
  ... (remaining 14704 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.96: 19721
        4.96 -     9.93: 51
        9.93 -    14.89: 0
       14.89 -    19.85: 4
       19.85 -    24.81: 2
  Bond angle restraints: 19778
  Sorted by residual:
  angle pdb=" C40 6OU A 703 "
        pdb=" C41 6OU A 703 "
        pdb=" C42 6OU A 703 "
      ideal   model   delta    sigma   weight residual
     127.56  152.37  -24.81 3.00e+00 1.11e-01 6.84e+01
  angle pdb=" C40 6OU A 702 "
        pdb=" C41 6OU A 702 "
        pdb=" C42 6OU A 702 "
      ideal   model   delta    sigma   weight residual
     127.56  152.10  -24.54 3.00e+00 1.11e-01 6.69e+01
  angle pdb=" O22 6OU A 702 "
        pdb=" P23 6OU A 702 "
        pdb=" O26 6OU A 702 "
      ideal   model   delta    sigma   weight residual
      93.95  110.79  -16.84 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" C39 6OU A 702 "
        pdb=" C40 6OU A 702 "
        pdb=" C41 6OU A 702 "
      ideal   model   delta    sigma   weight residual
     127.60  111.61   15.99 3.00e+00 1.11e-01 2.84e+01
  angle pdb=" O22 6OU A 703 "
        pdb=" P23 6OU A 703 "
        pdb=" O26 6OU A 703 "
      ideal   model   delta    sigma   weight residual
      93.95  109.65  -15.70 3.00e+00 1.11e-01 2.74e+01
  ... (remaining 19773 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.32: 8480
       29.32 -    58.63: 364
       58.63 -    87.95: 33
       87.95 -   117.26: 0
      117.26 -   146.58: 2
  Dihedral angle restraints: 8879
    sinusoidal: 3667
      harmonic: 5212
  Sorted by residual:
  dihedral pdb=" CA  ILE A 282 "
           pdb=" C   ILE A 282 "
           pdb=" N   MET A 283 "
           pdb=" CA  MET A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.27   29.73     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  ARG D 139 "
           pdb=" C   ARG D 139 "
           pdb=" N   MET D 140 "
           pdb=" CA  MET D 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.90   23.10     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" C07 6OU A 702 "
           pdb=" C08 6OU A 702 "
           pdb=" C09 6OU A 702 "
           pdb=" C10 6OU A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.90   33.32  146.58     1      3.00e+01 1.11e-03 1.96e+01
  ... (remaining 8876 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1731
       0.048 -    0.097: 402
       0.097 -    0.145: 97
       0.145 -    0.193: 13
       0.193 -    0.241: 3
  Chirality restraints: 2246
  Sorted by residual:
  chirality pdb=" C20 6OU A 702 "
            pdb=" C19 6OU A 702 "
            pdb=" C21 6OU A 702 "
            pdb=" O30 6OU A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.59   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  PHE A 174 "
            pdb=" N   PHE A 174 "
            pdb=" C   PHE A 174 "
            pdb=" CB  PHE A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  ILE E 156 "
            pdb=" N   ILE E 156 "
            pdb=" C   ILE E 156 "
            pdb=" CB  ILE E 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.42e-01
  ... (remaining 2243 not shown)

  Planarity restraints: 2468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA E 401 "   -0.197 2.00e-02 2.50e+03   1.52e-01 2.32e+02
        pdb=" C11 OLA E 401 "    0.088 2.00e-02 2.50e+03
        pdb=" C8  OLA E 401 "   -0.088 2.00e-02 2.50e+03
        pdb=" C9  OLA E 401 "    0.197 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 173 "    0.021 2.00e-02 2.50e+03   3.94e-02 1.55e+01
        pdb=" C   THR A 173 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   THR A 173 "    0.025 2.00e-02 2.50e+03
        pdb=" N   PHE A 174 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E  30 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO E  31 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO E  31 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO E  31 "    0.030 5.00e-02 4.00e+02
  ... (remaining 2465 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 260
        2.70 -     3.25: 14113
        3.25 -     3.80: 21907
        3.80 -     4.35: 26921
        4.35 -     4.90: 44883
  Nonbonded interactions: 108084
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 168 "
            pdb=" N   GLU C 169 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" O   PHE A 251 "
            pdb=" OG  SER A 255 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER A 421 "
            pdb=" O   TYR A 437 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" ND2 ASN C   7 "
            pdb=" OD1 ASP C  27 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OG1 THR A 451 "
            pdb=" O   MET A 455 "
     model   vdw
     2.259 3.040
  ... (remaining 108079 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and resid 1 through 334)
}

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:             4.320
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     14.390
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
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   0.137  14709  Z= 0.280
  Angle     :  0.791  24.814  19778  Z= 0.404
  Chirality :  0.044   0.241   2246
  Planarity :  0.005   0.152   2468
  Dihedral  : 15.495 146.576   5505
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  0.83 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.21), residues: 1779
  helix:  1.42 (0.17), residues: 998
  sheet: -0.51 (0.43), residues: 159
  loop : -1.81 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 212 
 TYR   0.022   0.001   TYR C 222 
 PHE   0.019   0.001   PHE A 124 
 TRP   0.028   0.002   TRP D 153 
 HIS   0.008   0.001   HIS C  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00491 /  0.28 (14709)
  covalent geometry    : angle       0.79097 /  0.40 (19778)
  hydrogen bonds       : bond        0.15782 /  9.80 (  793)
  hydrogen bonds       : angle       5.62434 /  4.02 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 231
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 THR cc_start: 0.7393 (m) cc_final: 0.7084 (p)
REVERT: C  215 PHE cc_start: 0.7535 (m-80) cc_final: 0.7254 (m-80)
REVERT: D  157 HIS cc_start: 0.5035 (t-90) cc_final: 0.4749 (t-90)
REVERT: E   18 PHE cc_start: 0.6522 (m-80) cc_final: 0.6121 (t80)
REVERT: E   23 MET cc_start: 0.7482 (tpp) cc_final: 0.7075 (tpp)
REVERT: E  110 LEU cc_start: 0.8446 (tp) cc_final: 0.8176 (tt)
REVERT: E  158 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7265 (tt)
  outliers start: 14
  outliers final: 2
  residues processed: 237
  average time/residue: 0.1209
  time to fit residues: 42.5306
Evaluate side-chains
  187 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 184
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  159 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    0.6980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 GLN
D  20 GLN
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  19 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.203970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.160203 restraints weight = 23539.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.155844 restraints weight = 37692.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.150089 restraints weight = 31398.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.147570 restraints weight = 32011.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.146193 restraints weight = 28100.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14709  Z= 0.173
  Angle     :  0.639   9.615  19778  Z= 0.331
  Chirality :  0.043   0.166   2246
  Planarity :  0.004   0.072   2468
  Dihedral  :  9.269 148.949   2001
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.72 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.21), residues: 1779
  helix:  1.46 (0.17), residues: 993
  sheet: -0.46 (0.44), residues: 156
  loop : -1.69 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 226 
 TYR   0.029   0.002   TYR E 151 
 PHE   0.019   0.002   PHE A 529 
 TRP   0.033   0.002   TRP D 220 
 HIS   0.012   0.001   HIS C 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.17 (14709)
  covalent geometry    : angle       0.63944 /  0.33 (19778)
  hydrogen bonds       : bond        0.06109 /  3.90 (  793)
  hydrogen bonds       : angle       4.79980 /  3.48 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 196
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 THR cc_start: 0.7615 (m) cc_final: 0.7161 (p)
REVERT: A  319 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7749 (mmtp)
REVERT: A  344 LEU cc_start: 0.8042 (mt) cc_final: 0.7739 (tp)
REVERT: E   18 PHE cc_start: 0.6681 (m-80) cc_final: 0.6116 (t80)
REVERT: E   23 MET cc_start: 0.7549 (tpp) cc_final: 0.7169 (tpp)
REVERT: E  157 HIS cc_start: 0.6459 (t70) cc_final: 0.6087 (t70)
  outliers start: 29
  outliers final: 20
  residues processed: 213
  average time/residue: 0.1197
  time to fit residues: 37.5012
Evaluate side-chains
  190 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  555 GLU
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain D residue   55 PHE
Chi-restraints excluded: chain D residue   80 ASN
Chi-restraints excluded: chain E residue  134 HIS
Chi-restraints excluded: chain E residue  227 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 162 optimal weight:    6.9990
   chunk 140 optimal weight:    7.9990
   chunk 115 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 151 optimal weight:    0.8980
   overall best weight:    1.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  20 GLN
** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  19 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.201034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.155690 restraints weight = 23639.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.151184 restraints weight = 37524.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.147831 restraints weight = 34029.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147537 restraints weight = 31692.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.145896 restraints weight = 27340.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  14709  Z= 0.203
  Angle     :  0.678  12.480  19778  Z= 0.350
  Chirality :  0.044   0.185   2246
  Planarity :  0.004   0.054   2468
  Dihedral  :  9.037 146.875   1997
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.37 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.21), residues: 1779
  helix:  1.27 (0.17), residues: 998
  sheet: -0.37 (0.43), residues: 163
  loop : -1.78 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 168 
 TYR   0.022   0.002   TYR E  57 
 PHE   0.022   0.002   PHE A 529 
 TRP   0.023   0.003   TRP D 220 
 HIS   0.012   0.001   HIS E 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00475 /  0.20 (14709)
  covalent geometry    : angle       0.67761 /  0.35 (19778)
  hydrogen bonds       : bond        0.06841 /  4.33 (  793)
  hydrogen bonds       : angle       4.74958 /  3.43 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 185
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8968 (tt)
REVERT: A  556 ASP cc_start: 0.7661 (t0) cc_final: 0.7438 (t0)
REVERT: C   50 LEU cc_start: 0.4274 (OUTLIER) cc_final: 0.4055 (mm)
REVERT: C  212 ARG cc_start: 0.8395 (ttt-90) cc_final: 0.8064 (ttt90)
REVERT: E   18 PHE cc_start: 0.6760 (m-80) cc_final: 0.6086 (t80)
REVERT: E   23 MET cc_start: 0.7613 (tpp) cc_final: 0.7290 (tpp)
REVERT: E  290 MET cc_start: 0.4341 (mmp) cc_final: 0.4072 (mmp)
  outliers start: 49
  outliers final: 36
  residues processed: 217
  average time/residue: 0.1133
  time to fit residues: 36.7986
Evaluate side-chains
  209 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 171
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  210 CYS
Chi-restraints excluded: chain D residue   55 PHE
Chi-restraints excluded: chain D residue   80 ASN
Chi-restraints excluded: chain E residue   80 ASN
Chi-restraints excluded: chain E residue  134 HIS
Chi-restraints excluded: chain E residue  256 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 115 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0470
   chunk 167 optimal weight:   20.0000
   chunk 26 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 89 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  20 GLN
D 157 HIS
E  19 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.204912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.163914 restraints weight = 23477.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.155989 restraints weight = 30304.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.149562 restraints weight = 31621.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.149915 restraints weight = 29716.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.148775 restraints weight = 23915.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14709  Z= 0.124
  Angle     :  0.590  11.020  19778  Z= 0.301
  Chirality :  0.041   0.151   2246
  Planarity :  0.003   0.057   2468
  Dihedral  :  8.288 146.411   1997
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.74 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.21), residues: 1779
  helix:  1.56 (0.17), residues: 997
  sheet: -0.42 (0.41), residues: 176
  loop : -1.67 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 109 
 TYR   0.024   0.001   TYR E 151 
 PHE   0.013   0.001   PHE A 529 
 TRP   0.028   0.003   TRP E 122 
 HIS   0.009   0.001   HIS C 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 (14709)
  covalent geometry    : angle       0.59033 /  0.30 (19778)
  hydrogen bonds       : bond        0.05433 /  3.50 (  793)
  hydrogen bonds       : angle       4.36479 /  3.16 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 194
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8704 (tt)
REVERT: A  319 LYS cc_start: 0.8210 (tppt) cc_final: 0.7745 (mmtp)
REVERT: A  534 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7035 (mp)
REVERT: A  556 ASP cc_start: 0.7549 (t0) cc_final: 0.7269 (t0)
REVERT: C  212 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.8173 (ttp80)
REVERT: D  153 TRP cc_start: 0.7025 (t-100) cc_final: 0.5693 (t-100)
REVERT: E   18 PHE cc_start: 0.6679 (m-80) cc_final: 0.6128 (t80)
REVERT: E   23 MET cc_start: 0.7483 (tpp) cc_final: 0.7176 (tpp)
REVERT: E  110 LEU cc_start: 0.9000 (tp) cc_final: 0.8763 (tt)
REVERT: E  226 ARG cc_start: 0.7547 (mmm160) cc_final: 0.7346 (mmm160)
  outliers start: 38
  outliers final: 24
  residues processed: 217
  average time/residue: 0.1185
  time to fit residues: 37.6839
Evaluate side-chains
  201 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 175
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  534 LEU
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  555 GLU
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain D residue   80 ASN
Chi-restraints excluded: chain E residue  134 HIS
Chi-restraints excluded: chain E residue  256 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 137 optimal weight:   10.0000
   chunk 161 optimal weight:   30.0000
   chunk 104 optimal weight:    3.9990
   chunk 162 optimal weight:    5.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  20 GLN
E  19 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.200424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.154029 restraints weight = 23591.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.149810 restraints weight = 36397.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.143327 restraints weight = 27982.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.139961 restraints weight = 32546.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.139166 restraints weight = 26925.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  14709  Z= 0.218
  Angle     :  0.690  11.977  19778  Z= 0.353
  Chirality :  0.044   0.162   2246
  Planarity :  0.004   0.097   2468
  Dihedral  :  8.504 140.566   1996
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.49 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.21), residues: 1779
  helix:  1.22 (0.17), residues: 999
  sheet: -0.46 (0.41), residues: 176
  loop : -1.71 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 109 
 TYR   0.023   0.002   TYR E 151 
 PHE   0.024   0.002   PHE A 529 
 TRP   0.049   0.003   TRP D 153 
 HIS   0.027   0.002   HIS D 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00514 /  0.22 (14709)
  covalent geometry    : angle       0.69025 /  0.35 (19778)
  hydrogen bonds       : bond        0.06977 /  4.42 (  793)
  hydrogen bonds       : angle       4.63941 /  3.34 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 176
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8974 (tt)
REVERT: A  534 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7824 (mp)
REVERT: A  556 ASP cc_start: 0.7696 (t0) cc_final: 0.7328 (t0)
REVERT: B   71 MET cc_start: 0.7506 (ppp) cc_final: 0.7255 (ppp)
REVERT: C   50 LEU cc_start: 0.4058 (OUTLIER) cc_final: 0.3755 (mm)
REVERT: E   18 PHE cc_start: 0.6777 (m-80) cc_final: 0.6158 (t80)
REVERT: E   23 MET cc_start: 0.7625 (tpp) cc_final: 0.7301 (tpp)
REVERT: E  110 LEU cc_start: 0.9129 (tp) cc_final: 0.8561 (tt)
  outliers start: 51
  outliers final: 37
  residues processed: 211
  average time/residue: 0.1039
  time to fit residues: 32.7143
Evaluate side-chains
  206 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  534 LEU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   29 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  210 CYS
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain D residue   80 ASN
Chi-restraints excluded: chain E residue  134 HIS
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  290 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 141 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 89 optimal weight:   20.0000
   chunk 78 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 GLN
C 160 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.203754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.159193 restraints weight = 23566.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.155415 restraints weight = 38621.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.152271 restraints weight = 31832.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.151116 restraints weight = 27624.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.149322 restraints weight = 27579.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14709  Z= 0.138
  Angle     :  0.635  11.774  19778  Z= 0.319
  Chirality :  0.042   0.190   2246
  Planarity :  0.004   0.076   2468
  Dihedral  :  8.076 139.960   1996
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.13 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.21), residues: 1779
  helix:  1.46 (0.17), residues: 998
  sheet: -0.40 (0.41), residues: 176
  loop : -1.64 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 109 
 TYR   0.023   0.001   TYR E 151 
 PHE   0.015   0.001   PHE A 529 
 TRP   0.032   0.003   TRP D 153 
 HIS   0.011   0.001   HIS D 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 (14709)
  covalent geometry    : angle       0.63500 /  0.32 (19778)
  hydrogen bonds       : bond        0.05806 /  3.69 (  793)
  hydrogen bonds       : angle       4.35650 /  3.12 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 179
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6334 (ppp) cc_final: 0.5851 (ppp)
REVERT: A   63 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8793 (tt)
REVERT: A  319 LYS cc_start: 0.8136 (tppt) cc_final: 0.7719 (mmtp)
REVERT: A  534 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7248 (mp)
REVERT: A  556 ASP cc_start: 0.7663 (t0) cc_final: 0.7288 (t0)
REVERT: C   50 LEU cc_start: 0.4347 (OUTLIER) cc_final: 0.4023 (mm)
REVERT: C  221 MET cc_start: 0.5561 (tmm) cc_final: 0.5248 (tmm)
REVERT: E   18 PHE cc_start: 0.6708 (m-80) cc_final: 0.6103 (t80)
REVERT: E   23 MET cc_start: 0.7494 (tpp) cc_final: 0.7213 (tpp)
REVERT: E   26 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7141 (tt)
REVERT: E  110 LEU cc_start: 0.8949 (tp) cc_final: 0.8642 (tt)
REVERT: E  226 ARG cc_start: 0.7537 (mmm160) cc_final: 0.7303 (mmm160)
  outliers start: 54
  outliers final: 38
  residues processed: 211
  average time/residue: 0.1072
  time to fit residues: 33.8530
Evaluate side-chains
  208 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 166
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  528 MET
Chi-restraints excluded: chain A residue  534 LEU
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   29 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  160 HIS
Chi-restraints excluded: chain C residue  210 CYS
Chi-restraints excluded: chain D residue   80 ASN
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  162 GLN
Chi-restraints excluded: chain D residue  197 TRP
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  290 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 83 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 89 optimal weight:    8.9990
   chunk 125 optimal weight:   30.0000
   chunk 55 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 76 optimal weight:    0.0670
   chunk 24 optimal weight:    0.4980
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.0522

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.202756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.156582 restraints weight = 23501.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.153516 restraints weight = 35295.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.148931 restraints weight = 31070.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.146913 restraints weight = 31156.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.145503 restraints weight = 28296.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14709  Z= 0.151
  Angle     :  0.656  14.424  19778  Z= 0.326
  Chirality :  0.043   0.227   2246
  Planarity :  0.003   0.066   2468
  Dihedral  :  7.943 135.170   1996
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.90 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.21), residues: 1779
  helix:  1.51 (0.17), residues: 990
  sheet: -0.33 (0.42), residues: 173
  loop : -1.53 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 109 
 TYR   0.023   0.002   TYR E 151 
 PHE   0.018   0.001   PHE A 529 
 TRP   0.025   0.002   TRP D 122 
 HIS   0.016   0.001   HIS C 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 (14709)
  covalent geometry    : angle       0.65587 /  0.33 (19778)
  hydrogen bonds       : bond        0.05898 /  3.75 (  793)
  hydrogen bonds       : angle       4.33421 /  3.11 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 174
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6459 (ppp) cc_final: 0.6093 (ppp)
REVERT: A   63 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8712 (tt)
REVERT: A  319 LYS cc_start: 0.8185 (tppt) cc_final: 0.7736 (mmtp)
REVERT: A  534 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7450 (mp)
REVERT: A  556 ASP cc_start: 0.7712 (t0) cc_final: 0.7312 (t0)
REVERT: B   71 MET cc_start: 0.7580 (ppp) cc_final: 0.6731 (mmp)
REVERT: B   74 MET cc_start: 0.8633 (tmm) cc_final: 0.8417 (tmm)
REVERT: B  112 ILE cc_start: 0.8840 (mm) cc_final: 0.8554 (mm)
REVERT: C   50 LEU cc_start: 0.4267 (OUTLIER) cc_final: 0.3918 (mm)
REVERT: E   18 PHE cc_start: 0.6730 (m-80) cc_final: 0.6121 (t80)
REVERT: E   23 MET cc_start: 0.7494 (tpp) cc_final: 0.7194 (tpp)
REVERT: E   26 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7138 (tt)
  outliers start: 52
  outliers final: 45
  residues processed: 206
  average time/residue: 0.0997
  time to fit residues: 31.0660
Evaluate side-chains
  220 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 171
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  511 LEU
Chi-restraints excluded: chain A residue  534 LEU
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   29 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  160 HIS
Chi-restraints excluded: chain C residue  210 CYS
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain D residue   80 ASN
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  155 ARG
Chi-restraints excluded: chain D residue  162 GLN
Chi-restraints excluded: chain D residue  197 TRP
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  290 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0870
   chunk 28 optimal weight:    0.0970
   chunk 78 optimal weight:    0.8980
   chunk 130 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4756

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 503 GLN
A 505 ASN
C 160 HIS
** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.205204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.159575 restraints weight = 23372.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.154018 restraints weight = 37607.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.150362 restraints weight = 30653.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.149304 restraints weight = 26010.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.148521 restraints weight = 21670.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14709  Z= 0.123
  Angle     :  0.655  15.598  19778  Z= 0.322
  Chirality :  0.042   0.206   2246
  Planarity :  0.003   0.068   2468
  Dihedral  :  7.546 127.320   1996
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.18 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.21), residues: 1779
  helix:  1.69 (0.17), residues: 990
  sheet: -0.28 (0.42), residues: 174
  loop : -1.45 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 109 
 TYR   0.023   0.001   TYR E 151 
 PHE   0.012   0.001   PHE A 529 
 TRP   0.031   0.002   TRP E 153 
 HIS   0.018   0.001   HIS D 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 (14709)
  covalent geometry    : angle       0.65494 /  0.32 (19778)
  hydrogen bonds       : bond        0.05127 /  3.31 (  793)
  hydrogen bonds       : angle       4.19190 /  2.98 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 189
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6395 (ppp) cc_final: 0.6141 (ppp)
REVERT: A   63 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8806 (tt)
REVERT: A  173 THR cc_start: 0.7518 (m) cc_final: 0.6940 (p)
REVERT: A  556 ASP cc_start: 0.7541 (t0) cc_final: 0.7164 (t0)
REVERT: B  112 ILE cc_start: 0.8814 (mm) cc_final: 0.8530 (mm)
REVERT: C   50 LEU cc_start: 0.4277 (OUTLIER) cc_final: 0.3953 (mm)
REVERT: E   18 PHE cc_start: 0.6701 (m-80) cc_final: 0.6153 (t80)
REVERT: E   23 MET cc_start: 0.7520 (tpp) cc_final: 0.7126 (tpp)
  outliers start: 44
  outliers final: 33
  residues processed: 216
  average time/residue: 0.1048
  time to fit residues: 34.0918
Evaluate side-chains
  213 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 178
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  555 GLU
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  160 HIS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  162 GLN
Chi-restraints excluded: chain D residue  197 TRP
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  290 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 117 optimal weight:    0.5980
   chunk 156 optimal weight:    0.0770
   chunk 21 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 67 optimal weight:    0.2980
   chunk 15 optimal weight:    0.8980
   chunk 133 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.205056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.160037 restraints weight = 23740.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.155197 restraints weight = 36478.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.149478 restraints weight = 30685.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.148595 restraints weight = 28741.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.148119 restraints weight = 21909.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14709  Z= 0.127
  Angle     :  0.688  16.015  19778  Z= 0.337
  Chirality :  0.043   0.229   2246
  Planarity :  0.003   0.069   2468
  Dihedral  :  7.387 120.403   1996
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.31 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.21), residues: 1779
  helix:  1.67 (0.17), residues: 990
  sheet: -0.32 (0.42), residues: 175
  loop : -1.44 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 109 
 TYR   0.024   0.001   TYR E 151 
 PHE   0.018   0.001   PHE E 223 
 TRP   0.031   0.002   TRP E 153 
 HIS   0.018   0.001   HIS D 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 (14709)
  covalent geometry    : angle       0.68756 /  0.34 (19778)
  hydrogen bonds       : bond        0.05169 /  3.33 (  793)
  hydrogen bonds       : angle       4.18245 /  2.97 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 179
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6393 (ppp) cc_final: 0.6183 (ppp)
REVERT: A   63 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8513 (tt)
REVERT: A  173 THR cc_start: 0.7439 (m) cc_final: 0.6913 (p)
REVERT: A  319 LYS cc_start: 0.7888 (tppt) cc_final: 0.7405 (mmtp)
REVERT: A  534 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7051 (mp)
REVERT: A  556 ASP cc_start: 0.7560 (t0) cc_final: 0.7182 (t0)
REVERT: B  112 ILE cc_start: 0.8825 (mm) cc_final: 0.8555 (mm)
REVERT: C   50 LEU cc_start: 0.4273 (OUTLIER) cc_final: 0.3952 (mm)
REVERT: D  155 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7515 (tpp80)
REVERT: D  290 MET cc_start: 0.6224 (mmm) cc_final: 0.5955 (mmm)
REVERT: E   18 PHE cc_start: 0.6719 (m-80) cc_final: 0.6102 (t80)
REVERT: E  140 MET cc_start: 0.3702 (ppp) cc_final: 0.2793 (ppp)
REVERT: E  226 ARG cc_start: 0.7677 (mmm160) cc_final: 0.7423 (mmm160)
  outliers start: 43
  outliers final: 34
  residues processed: 206
  average time/residue: 0.1110
  time to fit residues: 34.4591
Evaluate side-chains
  213 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  168 MET
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  534 LEU
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  555 GLU
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  125 GLU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  162 GLN
Chi-restraints excluded: chain D residue  197 TRP
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  290 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 36 optimal weight:    0.1980
   chunk 160 optimal weight:    0.6980
   chunk 144 optimal weight:    0.1980
   chunk 117 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 105 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 159 optimal weight:    0.7980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 114 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.206358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.162474 restraints weight = 23600.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.159864 restraints weight = 36578.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.155826 restraints weight = 27256.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.153411 restraints weight = 28367.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.152910 restraints weight = 24595.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14709  Z= 0.121
  Angle     :  0.673  16.506  19778  Z= 0.328
  Chirality :  0.042   0.224   2246
  Planarity :  0.003   0.070   2468
  Dihedral  :  7.084 107.336   1996
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.56 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.21), residues: 1779
  helix:  1.68 (0.17), residues: 997
  sheet: -0.33 (0.41), residues: 185
  loop : -1.31 (0.27), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 109 
 TYR   0.024   0.001   TYR E 151 
 PHE   0.013   0.001   PHE E 223 
 TRP   0.038   0.002   TRP E 153 
 HIS   0.015   0.001   HIS D 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 (14709)
  covalent geometry    : angle       0.67254 /  0.33 (19778)
  hydrogen bonds       : bond        0.04854 /  3.14 (  793)
  hydrogen bonds       : angle       4.09629 /  2.90 ( 2268)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 184
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8574 (tt)
REVERT: A  173 THR cc_start: 0.7428 (m) cc_final: 0.6946 (p)
REVERT: A  376 MET cc_start: 0.6062 (ppp) cc_final: 0.5798 (ppp)
REVERT: A  534 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6987 (mp)
REVERT: A  556 ASP cc_start: 0.7529 (t0) cc_final: 0.7168 (t0)
REVERT: C   50 LEU cc_start: 0.4254 (OUTLIER) cc_final: 0.3990 (mm)
REVERT: D  155 ARG cc_start: 0.7764 (tpp80) cc_final: 0.7521 (tpp80)
REVERT: E  140 MET cc_start: 0.3493 (ppp) cc_final: 0.2703 (ppp)
REVERT: E  226 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7358 (mmm160)
  outliers start: 41
  outliers final: 35
  residues processed: 207
  average time/residue: 0.1119
  time to fit residues: 35.2301
Evaluate side-chains
  219 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 181
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  168 MET
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  534 LEU
Chi-restraints excluded: chain A residue  541 THR
Chi-restraints excluded: chain A residue  555 GLU
Chi-restraints excluded: chain A residue  595 PHE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  210 CYS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  160 HIS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  197 TRP
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  290 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0980
   chunk 135 optimal weight:   40.0000
   chunk 168 optimal weight:   50.0000
   chunk 25 optimal weight:    0.2980
   chunk 159 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9990
   chunk 172 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.3980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.206742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.161661 restraints weight = 23658.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.156829 restraints weight = 34737.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.150983 restraints weight = 29319.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.149780 restraints weight = 27748.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.147830 restraints weight = 22337.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  14709  Z= 0.118
  Angle     :  0.677  15.889  19778  Z= 0.328
  Chirality :  0.042   0.212   2246
  Planarity :  0.003   0.070   2468
  Dihedral  :  6.844  93.816   1996
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.56 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.21), residues: 1779
  helix:  1.72 (0.17), residues: 997
  sheet: -0.22 (0.42), residues: 178
  loop : -1.32 (0.27), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D 109 
 TYR   0.024   0.001   TYR E 151 
 PHE   0.012   0.001   PHE A 529 
 TRP   0.036   0.002   TRP E 153 
 HIS   0.012   0.001   HIS D 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.12 (14709)
  covalent geometry    : angle       0.67678 /  0.33 (19778)
  hydrogen bonds       : bond        0.04707 /  3.03 (  793)
  hydrogen bonds       : angle       4.04642 /  2.86 ( 2268)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2285.09 seconds
wall clock time: 40 minutes 23.91 seconds (2423.91 seconds total)