Starting phenix.real_space_refine
on Sat Sep 12 00:09:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kuk_9578/09_2026/6kuk_9578_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kuk_9578/09_2026/6kuk_9578.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kuk_9578/09_2026/6kuk_9578_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kuk_9578/09_2026/6kuk_9578_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kuk_9578/09_2026/6kuk_9578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kuk_9578/09_2026/6kuk_9578.map"
  }
  resolution = 3.9
  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=   0.012
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      23      5.49       5
     S     109      5.16       5
     C    7695      2.51       5
     N    2091      2.21       5
     O    2326      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12244
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4176
          Classifications: {'peptide': 511}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 489}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 5568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 701, 5568
          Classifications: {'peptide': 701}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 25, 'TRANS': 675}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "C"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2006
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 11, 'TRANS': 237}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "R"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 163
          Classifications: {'RNA': 8}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 2, 'rna3p': 5}
    Chain: "V"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 331
          Classifications: {'RNA': 15}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 3, 'rna3p': 11}
  Time building chain proxies: 2.87, per 1000 atoms: 0.23
  Number of scatterers: 12244
  At special positions: 0
  Unit cell: (111.52, 110.16, 110.16, 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     109     16.00
     P      23     15.00
     O    2326      8.00
     N    2091      7.00
     C    7695      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: 1.00
  Conformation dependent library (CDL) restraints added in 517.8 milliseconds
  

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2766

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 12 sheets defined
      47.5% alpha, 7.8% beta
      7 base pairs and 14 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 191 through 198
      removed outlier: 3.774A  pdb=" N   ALA A 195 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 217
      removed outlier: 3.661A  pdb=" N   THR A 217 " --> pdb=" O   THR A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 234
      removed outlier: 4.103A  pdb=" N   SER A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 295
    Processing helix  chain 'A' and resid 296 through 300
      removed outlier: 3.710A  pdb=" N   PHE A 299 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 328
      removed outlier: 3.577A  pdb=" N   ASP A 328 " --> pdb=" O   ARG A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 343
    Processing helix  chain 'A' and resid 381 through 390
    Processing helix  chain 'A' and resid 416 through 432
    Processing helix  chain 'A' and resid 434 through 457
      removed outlier: 3.719A  pdb=" N   ARG A 438 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE A 457 " --> pdb=" O   GLU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 589
      removed outlier: 3.758A  pdb=" N   MET A 574 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 575 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 637
    Processing helix  chain 'A' and resid 639 through 661
      removed outlier: 3.831A  pdb=" N   GLU A 643 " --> pdb=" O   ASP A 639 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASP A 661 " --> pdb=" O   GLN A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 678
    Processing helix  chain 'A' and resid 684 through 703
    Processing helix  chain 'B' and resid 4 through 11
      removed outlier: 3.838A  pdb=" N   LEU B   7 " --> pdb=" O   ASN B   4 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LEU B   8 " --> pdb=" O   PRO B   5 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN B  11 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 3.843A  pdb=" N   TYR B  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 49
      removed outlier: 3.909A  pdb=" N   SER B  39 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 99
    Processing helix  chain 'B' and resid 104 through 118
    Processing helix  chain 'B' and resid 121 through 127
    Processing helix  chain 'B' and resid 141 through 157
    Processing helix  chain 'B' and resid 164 through 178
      removed outlier: 3.658A  pdb=" N   TYR B 168 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TRP B 178 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 250 through 268
    Processing helix  chain 'B' and resid 281 through 293
      removed outlier: 3.944A  pdb=" N   LYS B 285 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 314
      removed outlier: 3.579A  pdb=" N   GLU B 313 " --> pdb=" O   LYS B 310 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   CYS B 314 " --> pdb=" O   TRP B 311 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 310 through 314'
    Processing helix  chain 'B' and resid 316 through 328
      removed outlier: 3.822A  pdb=" N   TYR B 320 " --> pdb=" O   GLN B 316 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   THR B 328 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 339
    Processing helix  chain 'B' and resid 341 through 347
    Processing helix  chain 'B' and resid 378 through 382
      removed outlier: 3.605A  pdb=" N   LEU B 381 " --> pdb=" O   ARG B 378 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   MET B 382 " --> pdb=" O   LYS B 379 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 378 through 382'
    Processing helix  chain 'B' and resid 383 through 391
      removed outlier: 3.705A  pdb=" N   ARG B 387 " --> pdb=" O   ASN B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 397
    Processing helix  chain 'B' and resid 416 through 425
      removed outlier: 3.539A  pdb=" N   PHE B 420 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 475
    Processing helix  chain 'B' and resid 510 through 514
    Processing helix  chain 'B' and resid 523 through 537
    Processing helix  chain 'B' and resid 541 through 561
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 3.711A  pdb=" N   ILE B 577 " --> pdb=" O   ARG B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 584
    Processing helix  chain 'B' and resid 586 through 590
      removed outlier: 3.717A  pdb=" N   GLY B 589 " --> pdb=" O   ASN B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 595
    Processing helix  chain 'B' and resid 608 through 614
    Processing helix  chain 'B' and resid 618 through 626
    Processing helix  chain 'B' and resid 675 through 696
      removed outlier: 3.741A  pdb=" N   ALA B 679 " --> pdb=" O   MET B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 728
      removed outlier: 3.574A  pdb=" N   ASN B 728 " --> pdb=" O   THR B 724 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 732 through 752
    Processing helix  chain 'C' and resid 3 through 15
      removed outlier: 3.577A  pdb=" N   THR C  15 " --> pdb=" O   TYR C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 37
      removed outlier: 4.001A  pdb=" N   THR C  34 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS C  37 " --> pdb=" O   THR C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 56
    Processing helix  chain 'C' and resid 65 through 72
    Processing helix  chain 'C' and resid 99 through 109
    Processing helix  chain 'C' and resid 114 through 122
      removed outlier: 3.720A  pdb=" N   TYR C 122 " --> pdb=" O   ILE C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 134
      removed outlier: 3.726A  pdb=" N   GLU C 134 " --> pdb=" O   GLU C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 172
      removed outlier: 3.690A  pdb=" N   GLU C 168 " --> pdb=" O   LYS C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 179
      removed outlier: 4.391A  pdb=" N   GLU C 178 " --> pdb=" O   PHE C 175 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA C 179 " --> pdb=" O   GLU C 176 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 175 through 179'
    Processing helix  chain 'C' and resid 186 through 197
    Processing helix  chain 'C' and resid 206 through 215
      removed outlier: 4.078A  pdb=" N   ALA C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 236
    Processing helix  chain 'C' and resid 238 through 243
      removed outlier: 4.085A  pdb=" N   GLY C 243 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 276
      removed outlier: 3.690A  pdb=" N   LYS A 275 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASP A 478 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 353
      removed outlier: 5.656A  pdb=" N   LYS A 350 " --> pdb=" O   GLU B 367 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL B 369 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE A 352 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 466
      removed outlier: 6.533A  pdb=" N   LYS A 544 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   THR A 525 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU A 546 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 602 through 604
    Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56
    Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 133
    Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 185
    Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245
      removed outlier: 7.680A  pdb=" N   ILE B 226 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 491 through 492
    Processing sheet with id=AB2, first strand: chain 'B' and resid 663 through 664
      removed outlier: 4.706A  pdb=" N   ARG B 663 " --> pdb=" O   MET C  62 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 153

    506 hydrogen bonds defined for protein.
    1410 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      19 hydrogen bonds
      38 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      14 stacking parallelities
  Total time for adding SS restraints: 2.15

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3496
        1.33 -     1.46: 2456
        1.46 -     1.58: 6357
        1.58 -     1.70: 44
        1.70 -     1.82: 181
  Bond restraints: 12534
  Sorted by residual:
  bond pdb=" CA  ILE B 730 "
       pdb=" C   ILE B 730 "
    ideal  model  delta    sigma   weight residual
    1.523  1.461  0.062 1.27e-02 6.20e+03 2.41e+01
  bond pdb=" N7    A V   4 "
       pdb=" C5    A V   4 "
    ideal  model  delta    sigma   weight residual
    1.388  1.370  0.018 6.00e-03 2.78e+04 8.65e+00
  bond pdb=" N   ILE B 731 "
       pdb=" CA  ILE B 731 "
    ideal  model  delta    sigma   weight residual
    1.459  1.423  0.036 1.25e-02 6.40e+03 8.35e+00
  bond pdb=" N9    A V  10 "
       pdb=" C4    A V  10 "
    ideal  model  delta    sigma   weight residual
    1.374  1.358  0.016 6.00e-03 2.78e+04 6.71e+00
  bond pdb=" N3    A V   4 "
       pdb=" C4    A V   4 "
    ideal  model  delta    sigma   weight residual
    1.344  1.330  0.014 6.00e-03 2.78e+04 5.61e+00
  ... (remaining 12529 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 16094
        2.14 -     4.28: 749
        4.28 -     6.43: 76
        6.43 -     8.57: 24
        8.57 -    10.71: 5
  Bond angle restraints: 16948
  Sorted by residual:
  angle pdb=" N   ILE B 393 "
        pdb=" CA  ILE B 393 "
        pdb=" C   ILE B 393 "
      ideal   model   delta    sigma   weight residual
     113.20  105.82    7.38 9.60e-01 1.09e+00 5.90e+01
  angle pdb=" O5'   U R   5 "
        pdb=" C5'   U R   5 "
        pdb=" C4'   U R   5 "
      ideal   model   delta    sigma   weight residual
     109.40  113.83   -4.43 8.00e-01 1.56e+00 3.06e+01
  angle pdb=" O4'   A V   7 "
        pdb=" C1'   A V   7 "
        pdb=" N9    A V   7 "
      ideal   model   delta    sigma   weight residual
     108.20  112.19   -3.99 8.00e-01 1.56e+00 2.49e+01
  angle pdb=" O5'   A V   7 "
        pdb=" C5'   A V   7 "
        pdb=" C4'   A V   7 "
      ideal   model   delta    sigma   weight residual
     109.40  113.35   -3.95 8.00e-01 1.56e+00 2.44e+01
  angle pdb=" CA  LYS A 488 "
        pdb=" CB  LYS A 488 "
        pdb=" CG  LYS A 488 "
      ideal   model   delta    sigma   weight residual
     114.10  122.85   -8.75 2.00e+00 2.50e-01 1.92e+01
  ... (remaining 16943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.63: 7170
       15.63 -    31.26: 391
       31.26 -    46.89: 102
       46.89 -    62.51: 27
       62.51 -    78.14: 25
  Dihedral angle restraints: 7715
    sinusoidal: 3455
      harmonic: 4260
  Sorted by residual:
  dihedral pdb=" CA  ILE C 186 "
           pdb=" C   ILE C 186 "
           pdb=" N   GLN C 187 "
           pdb=" CA  GLN C 187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.88  -28.12     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  ASN B 728 "
           pdb=" C   ASN B 728 "
           pdb=" N   GLY B 729 "
           pdb=" CA  GLY B 729 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.49  -25.51     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  ILE A 604 "
           pdb=" C   ILE A 604 "
           pdb=" N   ALA A 605 "
           pdb=" CA  ALA A 605 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.00   25.00     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 7712 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1455
       0.072 -    0.143: 364
       0.143 -    0.214: 32
       0.214 -    0.286: 3
       0.286 -    0.357: 1
  Chirality restraints: 1855
  Sorted by residual:
  chirality pdb=" CB  ILE B 304 "
            pdb=" CA  ILE B 304 "
            pdb=" CG1 ILE B 304 "
            pdb=" CG2 ILE B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CB  ILE B  72 "
            pdb=" CA  ILE B  72 "
            pdb=" CG1 ILE B  72 "
            pdb=" CG2 ILE B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CB  ILE C 249 "
            pdb=" CA  ILE C 249 "
            pdb=" CG1 ILE C 249 "
            pdb=" CG2 ILE C 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1852 not shown)

  Planarity restraints: 2068
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 386 "   -0.020 2.00e-02 2.50e+03   1.70e-02 7.19e+00
        pdb=" CG  TRP A 386 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 386 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 386 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 386 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 386 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 386 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 386 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 386 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 386 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 155 "   -0.040 5.00e-02 4.00e+02   6.11e-02 5.98e+00
        pdb=" N   PRO C 156 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO C 156 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 156 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 731 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.08e+00
        pdb=" C   ILE B 731 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ILE B 731 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY B 732 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2065 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1419
        2.74 -     3.28: 11176
        3.28 -     3.82: 18742
        3.82 -     4.36: 22829
        4.36 -     4.90: 38857
  Nonbonded interactions: 93023
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 408 "
            pdb=" NH2 ARG B 557 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OH  TYR B  49 "
            pdb=" NZ  LYS B 310 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OD2 ASP B 615 "
            pdb=" NZ  LYS C 129 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" O   ALA B 152 "
            pdb=" OG1 THR B 156 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE1 GLN A 649 "
            pdb=" OH  TYR B   6 "
     model   vdw
     2.269 3.040
  ... (remaining 93018 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     13.200
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
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      :  0.008   0.074  12534  Z= 0.372
  Angle     :  1.036  10.708  16948  Z= 0.613
  Chirality :  0.060   0.357   1855
  Planarity :  0.007   0.061   2068
  Dihedral  : 11.980  78.142   4949
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.61 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  3.04 %
    Favored  : 96.49 %
  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: -4.88 (0.16), residues: 1441
  helix: -3.38 (0.12), residues: 646
  sheet: -2.14 (0.46), residues: 126
  loop : -3.25 (0.19), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 573 
 TYR   0.033   0.003   TYR B  38 
 PHE   0.033   0.004   PHE B 122 
 TRP   0.044   0.004   TRP A 386 
 HIS   0.012   0.003   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00791 /  0.37 (12534)
  covalent geometry    : angle       1.03575 /  0.61 (16948)
  hydrogen bonds       : bond        0.16545 / 10.83 (  525)
  hydrogen bonds       : angle       9.11073 /  6.30 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 450
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.8425 (tmmt) cc_final: 0.7937 (tmmt)
REVERT: A  277 HIS cc_start: 0.6382 (t70) cc_final: 0.6098 (t-90)
REVERT: A  278 ASP cc_start: 0.7021 (t0) cc_final: 0.6749 (t0)
REVERT: A  290 ASP cc_start: 0.7697 (m-30) cc_final: 0.7345 (m-30)
REVERT: A  364 GLU cc_start: 0.7887 (mp0) cc_final: 0.7496 (mp0)
REVERT: A  367 GLN cc_start: 0.6979 (pt0) cc_final: 0.6774 (mt0)
REVERT: A  495 ASP cc_start: 0.7719 (m-30) cc_final: 0.7312 (p0)
REVERT: A  650 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7694 (pttp)
REVERT: B   47 TYR cc_start: 0.8098 (m-10) cc_final: 0.7856 (m-10)
REVERT: B  140 MET cc_start: 0.7415 (mtt) cc_final: 0.7014 (mtt)
REVERT: B  147 GLN cc_start: 0.8496 (tp-100) cc_final: 0.7534 (tm-30)
REVERT: B  182 LYS cc_start: 0.7447 (mtmt) cc_final: 0.6930 (mtmm)
REVERT: B  490 LEU cc_start: 0.8707 (tp) cc_final: 0.8451 (tp)
REVERT: B  515 THR cc_start: 0.6793 (p) cc_final: 0.6547 (t)
REVERT: B  560 TYR cc_start: 0.7238 (m-80) cc_final: 0.6871 (m-80)
REVERT: B  578 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5185 (mtp180)
REVERT: B  685 TYR cc_start: 0.7534 (m-10) cc_final: 0.6901 (m-80)
REVERT: C   18 LYS cc_start: 0.7200 (mttt) cc_final: 0.6863 (tppt)
REVERT: C   65 ARG cc_start: 0.7065 (ttt90) cc_final: 0.6786 (ttm-80)
REVERT: C   80 ILE cc_start: 0.5637 (mt) cc_final: 0.4733 (mt)
REVERT: C  213 MET cc_start: 0.5011 (ptm) cc_final: 0.4581 (ptm)
  outliers start: 6
  outliers final: 1
  residues processed: 454
  average time/residue: 0.1299
  time to fit residues: 80.9696
Evaluate side-chains
  293 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 291
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  578 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0770
   chunk 122 optimal weight:    0.0770
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.5096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 316 HIS
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 HIS
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 631 GLN
A 647 ASN
B  84 ASN
B 147 GLN
B 154 GLN
B 303 ASN
B 312 ASN
B 477 ASN
C 148 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.176005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.146499 restraints weight = 17975.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.149607 restraints weight = 10885.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.151639 restraints weight = 7727.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.152992 restraints weight = 6171.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.153746 restraints weight = 5317.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12534  Z= 0.155
  Angle     :  0.713  17.088  16948  Z= 0.369
  Chirality :  0.044   0.220   1855
  Planarity :  0.005   0.059   2068
  Dihedral  : 11.851  73.942   1930
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.38 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 10.13 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.27 (0.19), residues: 1441
  helix: -1.51 (0.17), residues: 655
  sheet: -1.54 (0.49), residues: 119
  loop : -2.99 (0.20), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 131 
 TYR   0.017   0.001   TYR B 692 
 PHE   0.027   0.002   PHE B 108 
 TRP   0.014   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.16 (12534)
  covalent geometry    : angle       0.71307 /  0.37 (16948)
  hydrogen bonds       : bond        0.05852 /  3.93 (  525)
  hydrogen bonds       : angle       5.83444 /  4.01 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 335
  time to evaluate  : 0.399 
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  185 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8072 (pt)
REVERT: A  231 ASP cc_start: 0.8596 (t70) cc_final: 0.8184 (t70)
REVERT: A  277 HIS cc_start: 0.6277 (t70) cc_final: 0.6057 (t-90)
REVERT: A  367 GLN cc_start: 0.6748 (pt0) cc_final: 0.6532 (mt0)
REVERT: A  442 LYS cc_start: 0.9030 (tttt) cc_final: 0.8788 (tttm)
REVERT: A  653 LEU cc_start: 0.8934 (mm) cc_final: 0.8609 (mp)
REVERT: B  147 GLN cc_start: 0.8701 (tp40) cc_final: 0.7417 (tm-30)
REVERT: B  165 MET cc_start: 0.7104 (mmm) cc_final: 0.6822 (mmm)
REVERT: B  182 LYS cc_start: 0.7338 (mtmt) cc_final: 0.6946 (mtmm)
REVERT: B  423 MET cc_start: 0.8642 (mtm) cc_final: 0.8405 (mtp)
REVERT: B  515 THR cc_start: 0.6755 (p) cc_final: 0.6437 (t)
REVERT: B  560 TYR cc_start: 0.7290 (m-80) cc_final: 0.6902 (m-80)
REVERT: B  587 LYS cc_start: 0.7381 (mttt) cc_final: 0.7068 (mttt)
REVERT: B  685 TYR cc_start: 0.7594 (m-10) cc_final: 0.7217 (m-80)
REVERT: C   18 LYS cc_start: 0.7293 (mttt) cc_final: 0.6711 (tppt)
REVERT: C  213 MET cc_start: 0.5376 (ptm) cc_final: 0.4975 (ptm)
  outliers start: 41
  outliers final: 24
  residues processed: 356
  average time/residue: 0.1148
  time to fit residues: 58.3793
Evaluate side-chains
  299 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 274
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  692 ASP
Chi-restraints excluded: chain B residue   50 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain C residue    3 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 63 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 93 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 ASN
C 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.173324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143797 restraints weight = 18603.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.146820 restraints weight = 11283.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.148837 restraints weight = 8033.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150032 restraints weight = 6432.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.150972 restraints weight = 5560.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12534  Z= 0.153
  Angle     :  0.667  17.010  16948  Z= 0.341
  Chirality :  0.044   0.212   1855
  Planarity :  0.004   0.048   2068
  Dihedral  : 11.601  73.868   1926
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.45 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.33 %
    Favored  : 83.79 %
  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: -2.53 (0.20), residues: 1441
  helix: -0.79 (0.19), residues: 665
  sheet: -1.28 (0.48), residues: 130
  loop : -2.73 (0.21), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 741 
 TYR   0.042   0.002   TYR B 320 
 PHE   0.024   0.002   PHE B 108 
 TRP   0.015   0.001   TRP A 386 
 HIS   0.005   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 (12534)
  covalent geometry    : angle       0.66681 /  0.34 (16948)
  hydrogen bonds       : bond        0.05278 /  3.54 (  525)
  hydrogen bonds       : angle       5.27599 /  3.63 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 292
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8200 (pt)
REVERT: A  231 ASP cc_start: 0.8658 (t70) cc_final: 0.8294 (t70)
REVERT: A  318 LEU cc_start: 0.8857 (tp) cc_final: 0.8633 (tp)
REVERT: A  653 LEU cc_start: 0.8875 (mm) cc_final: 0.8543 (mt)
REVERT: B   98 GLU cc_start: 0.6817 (tp30) cc_final: 0.6560 (tp30)
REVERT: B  151 ASP cc_start: 0.7130 (m-30) cc_final: 0.6915 (m-30)
REVERT: B  165 MET cc_start: 0.7297 (mmm) cc_final: 0.7085 (mmm)
REVERT: B  182 LYS cc_start: 0.7139 (mtmt) cc_final: 0.6458 (mtmm)
REVERT: B  259 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7987 (t)
REVERT: B  337 ASP cc_start: 0.7837 (m-30) cc_final: 0.7555 (m-30)
REVERT: B  515 THR cc_start: 0.6767 (p) cc_final: 0.6428 (t)
REVERT: B  560 TYR cc_start: 0.7331 (m-80) cc_final: 0.6848 (m-80)
REVERT: B  587 LYS cc_start: 0.7356 (mttt) cc_final: 0.7062 (mttt)
REVERT: B  685 TYR cc_start: 0.7681 (m-10) cc_final: 0.7381 (m-80)
REVERT: C   18 LYS cc_start: 0.7304 (mttt) cc_final: 0.6679 (tppt)
REVERT: C   51 MET cc_start: 0.7495 (tpp) cc_final: 0.6552 (tpp)
REVERT: C   55 MET cc_start: 0.3978 (mmp) cc_final: 0.3654 (mmm)
REVERT: C  213 MET cc_start: 0.5450 (ptm) cc_final: 0.4998 (ptm)
  outliers start: 37
  outliers final: 25
  residues processed: 308
  average time/residue: 0.1006
  time to fit residues: 45.7873
Evaluate side-chains
  292 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 265
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain B residue    9 MET
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain B residue  743 ILE
Chi-restraints excluded: chain C residue    3 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0970
   chunk 119 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 142 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.1982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 640 ASN
B 147 GLN
B 303 ASN
B 534 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.172920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143434 restraints weight = 18405.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.146402 restraints weight = 11298.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.148343 restraints weight = 8117.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.149545 restraints weight = 6534.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.150413 restraints weight = 5676.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12534  Z= 0.150
  Angle     :  0.652  16.778  16948  Z= 0.331
  Chirality :  0.043   0.206   1855
  Planarity :  0.004   0.045   2068
  Dihedral  : 11.497  73.838   1926
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.87 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.11 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.23 (0.20), residues: 1441
  helix: -0.48 (0.19), residues: 676
  sheet: -1.13 (0.50), residues: 122
  loop : -2.68 (0.21), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 241 
 TYR   0.021   0.001   TYR B 320 
 PHE   0.021   0.002   PHE B 108 
 TRP   0.014   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 (12534)
  covalent geometry    : angle       0.65218 /  0.33 (16948)
  hydrogen bonds       : bond        0.05006 /  3.34 (  525)
  hydrogen bonds       : angle       5.03212 /  3.46 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 269
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7909 (pt)
REVERT: A  231 ASP cc_start: 0.8609 (t70) cc_final: 0.8139 (t70)
REVERT: A  426 GLU cc_start: 0.7974 (tp30) cc_final: 0.7705 (tm-30)
REVERT: A  653 LEU cc_start: 0.8843 (mm) cc_final: 0.8575 (mt)
REVERT: B   14 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8211 (tp)
REVERT: B   95 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6281 (mm-30)
REVERT: B  151 ASP cc_start: 0.7194 (m-30) cc_final: 0.6918 (m-30)
REVERT: B  320 TYR cc_start: 0.7748 (m-80) cc_final: 0.7376 (m-80)
REVERT: B  515 THR cc_start: 0.6772 (p) cc_final: 0.6425 (t)
REVERT: B  560 TYR cc_start: 0.7219 (m-80) cc_final: 0.6869 (m-80)
REVERT: B  587 LYS cc_start: 0.7481 (mttt) cc_final: 0.7152 (mttt)
REVERT: B  685 TYR cc_start: 0.7719 (m-10) cc_final: 0.7409 (m-80)
REVERT: C   18 LYS cc_start: 0.7289 (mttt) cc_final: 0.6664 (tppt)
REVERT: C   51 MET cc_start: 0.7480 (tpp) cc_final: 0.6742 (tpp)
REVERT: C  171 MET cc_start: 0.8222 (mmm) cc_final: 0.7359 (mtm)
REVERT: C  213 MET cc_start: 0.5443 (ptm) cc_final: 0.4983 (ptm)
  outliers start: 44
  outliers final: 31
  residues processed: 292
  average time/residue: 0.1043
  time to fit residues: 44.5901
Evaluate side-chains
  282 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 249
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  400 GLU
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain B residue  743 ILE
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 111 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 122 optimal weight:    9.9990
   chunk 143 optimal weight:    5.9990
   chunk 104 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 141 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 367 GLN
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 ASN
C 217 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.173578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.144439 restraints weight = 18363.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.147439 restraints weight = 11143.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.149333 restraints weight = 7965.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.150718 restraints weight = 6372.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.151474 restraints weight = 5479.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12534  Z= 0.137
  Angle     :  0.641  16.687  16948  Z= 0.326
  Chirality :  0.042   0.200   1855
  Planarity :  0.004   0.045   2068
  Dihedral  : 11.394  73.612   1926
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.80 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.65 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.00 (0.21), residues: 1441
  helix: -0.27 (0.19), residues: 687
  sheet: -1.09 (0.50), residues: 122
  loop : -2.60 (0.22), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 750 
 TYR   0.014   0.001   TYR B 320 
 PHE   0.039   0.002   PHE B 108 
 TRP   0.013   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 (12534)
  covalent geometry    : angle       0.64063 /  0.33 (16948)
  hydrogen bonds       : bond        0.04717 /  3.15 (  525)
  hydrogen bonds       : angle       4.88841 /  3.35 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 280
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7801 (pt)
REVERT: A  231 ASP cc_start: 0.8370 (t70) cc_final: 0.7862 (t70)
REVERT: A  235 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8156 (tpp-160)
REVERT: A  426 GLU cc_start: 0.7951 (tp30) cc_final: 0.7655 (tm-30)
REVERT: A  486 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8313 (mtpp)
REVERT: A  568 ARG cc_start: 0.8305 (ptp90) cc_final: 0.8014 (ptp90)
REVERT: A  653 LEU cc_start: 0.8834 (mm) cc_final: 0.8626 (mt)
REVERT: B    1 MET cc_start: 0.8574 (tmm) cc_final: 0.8322 (tmm)
REVERT: B   14 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8225 (tp)
REVERT: B   95 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6212 (mm-30)
REVERT: B  151 ASP cc_start: 0.7193 (m-30) cc_final: 0.6970 (m-30)
REVERT: B  182 LYS cc_start: 0.6527 (mttp) cc_final: 0.6098 (mtmm)
REVERT: B  320 TYR cc_start: 0.7700 (m-80) cc_final: 0.7342 (m-80)
REVERT: B  515 THR cc_start: 0.6634 (p) cc_final: 0.6329 (t)
REVERT: B  560 TYR cc_start: 0.7216 (m-80) cc_final: 0.6834 (m-80)
REVERT: B  587 LYS cc_start: 0.7506 (mttt) cc_final: 0.7199 (mttt)
REVERT: B  751 LEU cc_start: 0.8391 (tp) cc_final: 0.8050 (pp)
REVERT: C   18 LYS cc_start: 0.7604 (mttt) cc_final: 0.7006 (tppt)
REVERT: C   51 MET cc_start: 0.7325 (tpp) cc_final: 0.6443 (tpp)
REVERT: C   55 MET cc_start: 0.4481 (mmp) cc_final: 0.4243 (mmm)
REVERT: C   94 MET cc_start: 0.3585 (mmm) cc_final: 0.3344 (mmm)
REVERT: C  171 MET cc_start: 0.8053 (mmm) cc_final: 0.7230 (mtm)
REVERT: C  213 MET cc_start: 0.5351 (ptm) cc_final: 0.4910 (ptm)
  outliers start: 47
  outliers final: 31
  residues processed: 308
  average time/residue: 0.1039
  time to fit residues: 47.0594
Evaluate side-chains
  290 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 256
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  486 LYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain B residue    9 MET
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  400 GLU
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain B residue  743 ILE
Chi-restraints excluded: chain C residue    3 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 110 optimal weight:    5.9990
   chunk 136 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    1.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 GLN
B 303 ASN
C 141 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.172724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.143516 restraints weight = 18461.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.146455 restraints weight = 11321.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.148392 restraints weight = 8111.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.149586 restraints weight = 6507.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.150455 restraints weight = 5634.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12534  Z= 0.151
  Angle     :  0.647  16.821  16948  Z= 0.330
  Chirality :  0.043   0.193   1855
  Planarity :  0.004   0.044   2068
  Dihedral  : 11.359  73.696   1926
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.63 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.13 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.92 (0.21), residues: 1441
  helix: -0.17 (0.19), residues: 689
  sheet: -1.17 (0.49), residues: 126
  loop : -2.59 (0.22), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 748 
 TYR   0.011   0.001   TYR B 560 
 PHE   0.034   0.002   PHE B 108 
 TRP   0.014   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 (12534)
  covalent geometry    : angle       0.64738 /  0.33 (16948)
  hydrogen bonds       : bond        0.04748 /  3.16 (  525)
  hydrogen bonds       : angle       4.85548 /  3.31 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 264
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ASP cc_start: 0.8542 (t70) cc_final: 0.8017 (t70)
REVERT: A  235 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.8148 (tpp-160)
REVERT: A  353 GLN cc_start: 0.7181 (mp10) cc_final: 0.6769 (mp10)
REVERT: A  421 LYS cc_start: 0.7465 (tttm) cc_final: 0.7258 (tttm)
REVERT: A  426 GLU cc_start: 0.7976 (tp30) cc_final: 0.7680 (tm-30)
REVERT: A  568 ARG cc_start: 0.8413 (ptp90) cc_final: 0.8122 (ptp90)
REVERT: B   14 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8272 (tp)
REVERT: B   95 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6511 (mm-30)
REVERT: B  140 MET cc_start: 0.7225 (mtt) cc_final: 0.6988 (mtt)
REVERT: B  147 GLN cc_start: 0.8752 (tp40) cc_final: 0.8519 (tp-100)
REVERT: B  151 ASP cc_start: 0.7088 (m-30) cc_final: 0.6881 (m-30)
REVERT: B  165 MET cc_start: 0.7551 (mmm) cc_final: 0.7171 (mmm)
REVERT: B  182 LYS cc_start: 0.6556 (mttp) cc_final: 0.6093 (mtmm)
REVERT: B  320 TYR cc_start: 0.7701 (m-80) cc_final: 0.7318 (m-80)
REVERT: B  382 MET cc_start: 0.7387 (mtp) cc_final: 0.7012 (ttm)
REVERT: B  515 THR cc_start: 0.6749 (p) cc_final: 0.6433 (t)
REVERT: B  560 TYR cc_start: 0.7266 (m-80) cc_final: 0.6798 (m-80)
REVERT: B  587 LYS cc_start: 0.7566 (mttt) cc_final: 0.7249 (mttt)
REVERT: C   18 LYS cc_start: 0.7628 (mttt) cc_final: 0.6982 (tppt)
REVERT: C   51 MET cc_start: 0.7400 (tpp) cc_final: 0.6436 (tpp)
REVERT: C   55 MET cc_start: 0.4333 (mmp) cc_final: 0.3919 (mmm)
REVERT: C  171 MET cc_start: 0.8031 (mmm) cc_final: 0.7327 (mtm)
REVERT: C  213 MET cc_start: 0.5326 (ptm) cc_final: 0.4933 (ptm)
  outliers start: 48
  outliers final: 39
  residues processed: 292
  average time/residue: 0.1100
  time to fit residues: 46.9078
Evaluate side-chains
  282 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 242
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  269 ASP
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain B residue  743 ILE
Chi-restraints excluded: chain C residue    3 LEU
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0000
   chunk 134 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 110 optimal weight:    0.8980
   chunk 93 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    0.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 ASN
C 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.174806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.145633 restraints weight = 18199.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.148572 restraints weight = 11156.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.150549 restraints weight = 7998.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.151731 restraints weight = 6401.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.152612 restraints weight = 5554.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12534  Z= 0.123
  Angle     :  0.629  17.214  16948  Z= 0.320
  Chirality :  0.042   0.194   1855
  Planarity :  0.004   0.044   2068
  Dihedral  : 11.301  73.664   1926
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.52 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.69 %
    Favored  : 79.35 %
  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: -1.71 (0.21), residues: 1441
  helix: -0.03 (0.19), residues: 696
  sheet: -1.03 (0.51), residues: 117
  loop : -2.47 (0.22), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 750 
 TYR   0.011   0.001   TYR B 560 
 PHE   0.033   0.001   PHE B 108 
 TRP   0.014   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 490 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 (12534)
  covalent geometry    : angle       0.62930 /  0.32 (16948)
  hydrogen bonds       : bond        0.04391 /  2.92 (  525)
  hydrogen bonds       : angle       4.73059 /  3.23 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 275
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ASP cc_start: 0.8449 (t70) cc_final: 0.7979 (t70)
REVERT: A  353 GLN cc_start: 0.7200 (mp10) cc_final: 0.6796 (mp10)
REVERT: A  426 GLU cc_start: 0.7964 (tp30) cc_final: 0.7520 (tm-30)
REVERT: A  568 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7936 (ptp90)
REVERT: A  650 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7758 (ptpp)
REVERT: B   14 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8280 (tp)
REVERT: B   95 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6510 (mm-30)
REVERT: B   98 GLU cc_start: 0.7127 (tp30) cc_final: 0.6587 (tm-30)
REVERT: B  165 MET cc_start: 0.7496 (mmm) cc_final: 0.7102 (mmm)
REVERT: B  182 LYS cc_start: 0.6517 (mttp) cc_final: 0.6097 (mtmm)
REVERT: B  222 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7364 (mmm-85)
REVERT: B  320 TYR cc_start: 0.7764 (m-80) cc_final: 0.7204 (m-80)
REVERT: B  382 MET cc_start: 0.7212 (mtp) cc_final: 0.6953 (ttm)
REVERT: B  515 THR cc_start: 0.6832 (p) cc_final: 0.6513 (t)
REVERT: B  560 TYR cc_start: 0.7209 (m-80) cc_final: 0.6769 (m-80)
REVERT: B  587 LYS cc_start: 0.7578 (mttt) cc_final: 0.7253 (mttt)
REVERT: C   18 LYS cc_start: 0.7619 (mttt) cc_final: 0.6963 (tppt)
REVERT: C   51 MET cc_start: 0.7583 (tpp) cc_final: 0.6741 (tpp)
REVERT: C   55 MET cc_start: 0.4225 (mmp) cc_final: 0.3825 (mmm)
REVERT: C   65 ARG cc_start: 0.7166 (ttt90) cc_final: 0.6910 (ttm-80)
REVERT: C  131 ARG cc_start: 0.8247 (mtm110) cc_final: 0.8036 (mtm110)
REVERT: C  171 MET cc_start: 0.7997 (mmm) cc_final: 0.7324 (mtm)
REVERT: C  213 MET cc_start: 0.5349 (ptm) cc_final: 0.4966 (ptm)
  outliers start: 38
  outliers final: 28
  residues processed: 299
  average time/residue: 0.1147
  time to fit residues: 49.4056
Evaluate side-chains
  284 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 255
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  415 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   50 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 114 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 136 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 109 optimal weight:    6.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 GLN
B 303 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.174431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145335 restraints weight = 18270.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.148199 restraints weight = 11254.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.150120 restraints weight = 8113.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.151399 restraints weight = 6521.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.152075 restraints weight = 5683.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.4178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  12534  Z= 0.126
  Angle     :  0.628  17.332  16948  Z= 0.316
  Chirality :  0.042   0.190   1855
  Planarity :  0.004   0.044   2068
  Dihedral  : 11.253  73.689   1926
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.52 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.93 %
    Favored  : 78.88 %
  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: -1.52 (0.21), residues: 1441
  helix:  0.20 (0.20), residues: 691
  sheet: -0.99 (0.51), residues: 117
  loop : -2.43 (0.22), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 235 
 TYR   0.011   0.001   TYR B 560 
 PHE   0.022   0.001   PHE B 108 
 TRP   0.014   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 (12534)
  covalent geometry    : angle       0.62845 /  0.32 (16948)
  hydrogen bonds       : bond        0.04271 /  2.84 (  525)
  hydrogen bonds       : angle       4.68492 /  3.20 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 271
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.7663 (mptt) cc_final: 0.7328 (mmtm)
REVERT: A  426 GLU cc_start: 0.7961 (tp30) cc_final: 0.7576 (tm-30)
REVERT: A  455 ARG cc_start: 0.7732 (tpt170) cc_final: 0.7235 (tpm170)
REVERT: A  568 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7972 (ptp90)
REVERT: A  659 ASP cc_start: 0.8301 (t0) cc_final: 0.8066 (t0)
REVERT: B   14 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8271 (tp)
REVERT: B   95 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6488 (mm-30)
REVERT: B   98 GLU cc_start: 0.7088 (tp30) cc_final: 0.6760 (tp30)
REVERT: B  140 MET cc_start: 0.6903 (mtt) cc_final: 0.6592 (mtt)
REVERT: B  165 MET cc_start: 0.7463 (mmm) cc_final: 0.7138 (mmm)
REVERT: B  182 LYS cc_start: 0.6540 (mttp) cc_final: 0.6097 (mtmm)
REVERT: B  222 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7332 (mmm-85)
REVERT: B  320 TYR cc_start: 0.7747 (m-80) cc_final: 0.7105 (m-80)
REVERT: B  382 MET cc_start: 0.7333 (mtp) cc_final: 0.7033 (ttm)
REVERT: B  515 THR cc_start: 0.6809 (p) cc_final: 0.6527 (t)
REVERT: B  560 TYR cc_start: 0.7229 (m-80) cc_final: 0.6777 (m-80)
REVERT: B  587 LYS cc_start: 0.7637 (mttt) cc_final: 0.7315 (mttt)
REVERT: C   18 LYS cc_start: 0.7632 (mttt) cc_final: 0.6963 (tppt)
REVERT: C   51 MET cc_start: 0.7646 (tpp) cc_final: 0.6832 (tpp)
REVERT: C   55 MET cc_start: 0.4233 (mmp) cc_final: 0.3861 (mmm)
REVERT: C   65 ARG cc_start: 0.7285 (ttt90) cc_final: 0.7018 (ttm-80)
REVERT: C  131 ARG cc_start: 0.8278 (mtm110) cc_final: 0.8011 (mtm110)
REVERT: C  171 MET cc_start: 0.8150 (mmm) cc_final: 0.7452 (mtm)
REVERT: C  213 MET cc_start: 0.5419 (ptm) cc_final: 0.5054 (ptm)
  outliers start: 41
  outliers final: 35
  residues processed: 296
  average time/residue: 0.1166
  time to fit residues: 49.4227
Evaluate side-chains
  290 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 254
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   50 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  303 ASN
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain C residue    3 LEU
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 137 optimal weight:    0.0980
   chunk 124 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 143 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 120 optimal weight:    5.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.174626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.145612 restraints weight = 18353.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.148605 restraints weight = 11173.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.150518 restraints weight = 7972.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.151711 restraints weight = 6380.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.152606 restraints weight = 5538.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  12534  Z= 0.127
  Angle     :  0.634  17.331  16948  Z= 0.319
  Chirality :  0.041   0.190   1855
  Planarity :  0.004   0.045   2068
  Dihedral  : 11.239  73.691   1926
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.04 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.16 %
    Favored  : 79.11 %
  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: -1.48 (0.21), residues: 1441
  helix:  0.22 (0.20), residues: 692
  sheet: -1.05 (0.51), residues: 117
  loop : -2.39 (0.22), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 241 
 TYR   0.011   0.001   TYR B 560 
 PHE   0.026   0.001   PHE C  35 
 TRP   0.053   0.002   TRP A 388 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 (12534)
  covalent geometry    : angle       0.63374 /  0.32 (16948)
  hydrogen bonds       : bond        0.04255 /  2.81 (  525)
  hydrogen bonds       : angle       4.65787 /  3.18 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 266
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 ARG cc_start: 0.8171 (tpp-160) cc_final: 0.7942 (tpp-160)
REVERT: A  455 ARG cc_start: 0.7832 (tpt170) cc_final: 0.7285 (tpm170)
REVERT: A  601 ARG cc_start: 0.8295 (mmt180) cc_final: 0.8058 (mtp85)
REVERT: A  659 ASP cc_start: 0.8292 (t0) cc_final: 0.8073 (t0)
REVERT: B   14 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8281 (tp)
REVERT: B   95 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6429 (mm-30)
REVERT: B   98 GLU cc_start: 0.7052 (tp30) cc_final: 0.6735 (tp30)
REVERT: B  140 MET cc_start: 0.7061 (mtt) cc_final: 0.6707 (mtt)
REVERT: B  165 MET cc_start: 0.7557 (mmm) cc_final: 0.7249 (mmm)
REVERT: B  182 LYS cc_start: 0.6535 (mttp) cc_final: 0.6078 (mtmm)
REVERT: B  222 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7320 (mmm-85)
REVERT: B  263 LYS cc_start: 0.8360 (tptp) cc_final: 0.8074 (tppt)
REVERT: B  320 TYR cc_start: 0.7801 (m-80) cc_final: 0.7169 (m-80)
REVERT: B  382 MET cc_start: 0.7321 (mtp) cc_final: 0.7120 (ttm)
REVERT: B  515 THR cc_start: 0.6798 (p) cc_final: 0.6519 (t)
REVERT: B  560 TYR cc_start: 0.7273 (m-80) cc_final: 0.6788 (m-80)
REVERT: B  587 LYS cc_start: 0.7625 (mttt) cc_final: 0.7307 (mttt)
REVERT: C   18 LYS cc_start: 0.7643 (mttt) cc_final: 0.6970 (tppt)
REVERT: C   51 MET cc_start: 0.7606 (tpp) cc_final: 0.6852 (tpp)
REVERT: C   55 MET cc_start: 0.4215 (mmp) cc_final: 0.3855 (mmm)
REVERT: C   65 ARG cc_start: 0.7348 (ttt90) cc_final: 0.7060 (ttm-80)
REVERT: C  131 ARG cc_start: 0.8271 (mtm110) cc_final: 0.8007 (mtm110)
REVERT: C  171 MET cc_start: 0.8152 (mmm) cc_final: 0.7471 (mtm)
REVERT: C  213 MET cc_start: 0.5422 (ptm) cc_final: 0.5063 (ptm)
  outliers start: 35
  outliers final: 30
  residues processed: 288
  average time/residue: 0.1102
  time to fit residues: 45.9627
Evaluate side-chains
  287 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 256
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   50 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9980
   chunk 96 optimal weight:    0.0970
   chunk 116 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0050
   chunk 21 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.175395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.146136 restraints weight = 18474.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.149032 restraints weight = 11295.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.150936 restraints weight = 8120.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.151992 restraints weight = 6532.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.152970 restraints weight = 5722.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  12534  Z= 0.123
  Angle     :  0.654  17.595  16948  Z= 0.326
  Chirality :  0.042   0.190   1855
  Planarity :  0.004   0.045   2068
  Dihedral  : 11.220  73.691   1926
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.97 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.02 %
    Favored  : 78.57 %
  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: -1.42 (0.22), residues: 1441
  helix:  0.27 (0.20), residues: 693
  sheet: -1.08 (0.51), residues: 119
  loop : -2.34 (0.22), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 568 
 TYR   0.012   0.001   TYR A 188 
 PHE   0.021   0.001   PHE B 108 
 TRP   0.098   0.002   TRP A 388 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 (12534)
  covalent geometry    : angle       0.65422 /  0.33 (16948)
  hydrogen bonds       : bond        0.04076 /  2.70 (  525)
  hydrogen bonds       : angle       4.59511 /  3.15 ( 1448)

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

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

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2882 Ramachandran restraints generated.
    1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 263
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 LYS cc_start: 0.7643 (mptt) cc_final: 0.7333 (mmtm)
REVERT: A  455 ARG cc_start: 0.7785 (tpt170) cc_final: 0.7292 (tpm170)
REVERT: A  601 ARG cc_start: 0.8284 (mmt180) cc_final: 0.8027 (mtp85)
REVERT: A  653 LEU cc_start: 0.8970 (mp) cc_final: 0.8585 (mp)
REVERT: B   14 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8323 (tp)
REVERT: B   95 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6405 (mm-30)
REVERT: B   98 GLU cc_start: 0.7094 (tp30) cc_final: 0.6713 (tp30)
REVERT: B  140 MET cc_start: 0.7049 (mtt) cc_final: 0.6677 (mtt)
REVERT: B  161 LYS cc_start: 0.7528 (mmtt) cc_final: 0.6396 (ttmt)
REVERT: B  165 MET cc_start: 0.7536 (mmm) cc_final: 0.7209 (mmm)
REVERT: B  222 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7382 (mmm-85)
REVERT: B  241 ARG cc_start: 0.7365 (ttp-110) cc_final: 0.6915 (ttp-170)
REVERT: B  263 LYS cc_start: 0.8318 (tptp) cc_final: 0.7631 (ttmm)
REVERT: B  320 TYR cc_start: 0.7754 (m-80) cc_final: 0.7143 (m-80)
REVERT: B  410 MET cc_start: 0.5202 (mtp) cc_final: 0.4977 (mtp)
REVERT: B  474 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8032 (mtp)
REVERT: B  515 THR cc_start: 0.6746 (p) cc_final: 0.6483 (t)
REVERT: B  560 TYR cc_start: 0.7247 (m-80) cc_final: 0.6797 (m-80)
REVERT: B  587 LYS cc_start: 0.7489 (mttt) cc_final: 0.7210 (mttt)
REVERT: C   18 LYS cc_start: 0.7661 (mttt) cc_final: 0.7000 (tppt)
REVERT: C   51 MET cc_start: 0.7585 (tpp) cc_final: 0.6823 (tpp)
REVERT: C   55 MET cc_start: 0.4286 (mmp) cc_final: 0.4022 (mmm)
REVERT: C  141 ASN cc_start: 0.7023 (t0) cc_final: 0.6785 (t0)
REVERT: C  171 MET cc_start: 0.8144 (mmm) cc_final: 0.7454 (mtm)
REVERT: C  213 MET cc_start: 0.5443 (ptm) cc_final: 0.5056 (ptm)
  outliers start: 31
  outliers final: 26
  residues processed: 282
  average time/residue: 0.1126
  time to fit residues: 46.1370
Evaluate side-chains
  280 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 252
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  596 MET
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   50 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  508 LEU
Chi-restraints excluded: chain B residue  705 ILE
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  249 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 11 optimal weight:    0.0370
   chunk 23 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 57 optimal weight:    0.4980
   chunk 82 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 128 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.175588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.146457 restraints weight = 18414.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.149318 restraints weight = 11230.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.151281 restraints weight = 8073.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.152589 restraints weight = 6464.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.153202 restraints weight = 5581.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.4469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  12534  Z= 0.118
  Angle     :  0.629  17.694  16948  Z= 0.315
  Chirality :  0.041   0.189   1855
  Planarity :  0.004   0.049   2068
  Dihedral  : 11.199  73.673   1926
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.04 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.94 %
    Favored  : 78.49 %
  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: -1.34 (0.22), residues: 1441
  helix:  0.34 (0.20), residues: 692
  sheet: -1.03 (0.51), residues: 119
  loop : -2.30 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 568 
 TYR   0.011   0.001   TYR B 560 
 PHE   0.020   0.001   PHE B 108 
 TRP   0.092   0.002   TRP A 388 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 (12534)
  covalent geometry    : angle       0.62868 /  0.32 (16948)
  hydrogen bonds       : bond        0.04041 /  2.67 (  525)
  hydrogen bonds       : angle       4.54485 /  3.12 ( 1448)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2175.82 seconds
wall clock time: 38 minutes 25.95 seconds (2305.95 seconds total)