Starting phenix.real_space_refine
on Mon Jul 28 13:20:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pm1_13509/07_2025/7pm1_13509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pm1_13509/07_2025/7pm1_13509.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pm1_13509/07_2025/7pm1_13509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pm1_13509/07_2025/7pm1_13509.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pm1_13509/07_2025/7pm1_13509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pm1_13509/07_2025/7pm1_13509.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     Br      1      7.06       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      62      5.16       5
     C    6482      2.51       5
     N    1723      2.21       5
     O    1897      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10169
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1059
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 6130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 751, 6130
          Classifications: {'peptide': 751}
          Link IDs: {'PTRANS': 27, 'TRANS': 723}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2900
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 80
          Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 6.53, per 1000 atoms: 0.64
  Number of scatterers: 10169
  At special positions: 0
  Unit cell: (107.8, 130.9, 151.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Br      1     34.99
     S      62     16.00
     P       3     15.00
     Mg      1     11.99
     O    1897      8.00
     N    1723      7.00
     C    6482      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.50
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2374

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 14 sheets defined
      55.4% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.260A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   ASP B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 56 through 63
    Processing helix  chain 'B' and resid 67 through 79
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 87 through 95
    Processing helix  chain 'B' and resid 105 through 116
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 140 through 150
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 3.532A  pdb=" N   LEU A  77 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 95
      removed outlier: 3.519A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 119
      removed outlier: 4.348A  pdb=" N   TYR A 119 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 116 through 119'
    Processing helix  chain 'A' and resid 120 through 129
      removed outlier: 4.221A  pdb=" N   GLY A 129 " --> pdb=" O   ASN A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 3.675A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 184
    Processing helix  chain 'A' and resid 192 through 207
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 245 through 250
      removed outlier: 3.532A  pdb=" N   VAL A 249 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL A 250 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 3.980A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 278
      Proline residue:  A 272  - end of helix
      removed outlier: 4.768A  pdb=" N   THR A 276 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 4.112A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 315
      removed outlier: 3.695A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASN A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.840A  pdb=" N   MET A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 376
      removed outlier: 3.522A  pdb=" N   CYS A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 424
      removed outlier: 3.712A  pdb=" N   ASN A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 480
      removed outlier: 3.545A  pdb=" N   GLN A 464 " --> pdb=" O   LYS A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 487
      removed outlier: 3.612A  pdb=" N   LEU A 486 " --> pdb=" O   PRO A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 500
      removed outlier: 3.757A  pdb=" N   LEU A 498 " --> pdb=" O   PRO A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 515
    Processing helix  chain 'A' and resid 519 through 531
      removed outlier: 4.216A  pdb=" N   ASN A 529 " --> pdb=" O   GLN A 525 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   THR A 530 " --> pdb=" O   LYS A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
      removed outlier: 3.518A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU A 580 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 593
      removed outlier: 3.819A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 653
      removed outlier: 3.569A  pdb=" N   HIS A 645 " --> pdb=" O   ARG A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 685
      removed outlier: 3.758A  pdb=" N   GLN A 680 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 695
    Processing helix  chain 'A' and resid 704 through 712
    Processing helix  chain 'A' and resid 723 through 736
      removed outlier: 4.381A  pdb=" N   LYS A 729 " --> pdb=" O   LYS A 725 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASN A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 731 " --> pdb=" O   THR A 727 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 754 through 792
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 92
      removed outlier: 3.834A  pdb=" N   MET C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.534A  pdb=" N   HIS C 101 " --> pdb=" O   PRO C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 127
      removed outlier: 4.018A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET C 123 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
      removed outlier: 3.725A  pdb=" N   SER C 141 " --> pdb=" O   GLN C 137 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   TYR C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 181 through 194
      removed outlier: 3.594A  pdb=" N   THR C 194 " --> pdb=" O   MET C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 197
      No H-bonds generated for 'chain 'C' and resid 195 through 197'
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.735A  pdb=" N   ASP C 211 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
      removed outlier: 3.647A  pdb=" N   GLU C 226 " --> pdb=" O   ASP C 222 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA C 231 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 237
    Processing helix  chain 'C' and resid 252 through 263
      Proline residue:  C 258  - end of helix
      removed outlier: 4.580A  pdb=" N   LEU C 261 " --> pdb=" O   CYS C 257 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   PHE C 262 " --> pdb=" O   PRO C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 284
    Processing helix  chain 'C' and resid 286 through 296
      removed outlier: 4.623A  pdb=" N   LYS C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 3.651A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 321
      removed outlier: 3.578A  pdb=" N   THR C 318 " --> pdb=" O   GLN C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 336
      removed outlier: 4.459A  pdb=" N   LYS C 336 " --> pdb=" O   PRO C 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 349
    Processing helix  chain 'C' and resid 351 through 355
      removed outlier: 3.505A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 368 through 374
      removed outlier: 3.763A  pdb=" N   ARG C 372 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 15
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103
      removed outlier: 6.419A  pdb=" N   LEU A 107 " --> pdb=" O   ARG A 660 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   ILE A 662 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ALA A 109 " --> pdb=" O   ILE A 662 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   SER A 158 " --> pdb=" O   HIS A 657 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   CYS A 661 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 661 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY A 163 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 211
      removed outlier: 5.680A  pdb=" N   ALA A 209 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASN A 216 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342
    Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382
    Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703
      removed outlier: 3.722A  pdb=" N   SER A 700 " --> pdb=" O   PHE A 751 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.899A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   ASN C  12 " --> pdb=" O   THR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170
      removed outlier: 6.447A  pdb=" N   ILE C 151 " --> pdb=" O   VAL C 298 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   SER C 300 " --> pdb=" O   ILE C 151 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU C 153 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241

    507 hydrogen bonds defined for protein.
    1422 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.39

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2873
        1.33 -     1.47: 2857
        1.47 -     1.60: 4551
        1.60 -     1.73: 3
        1.73 -     1.87: 102
  Bond restraints: 10386
  Sorted by residual:
  bond pdb=" O4  PO4 C 402 "
       pdb=" P   PO4 C 402 "
    ideal  model  delta    sigma   weight residual
    1.568  1.507  0.061 2.00e-02 2.50e+03 9.28e+00
  bond pdb=" O3  PO4 C 402 "
       pdb=" P   PO4 C 402 "
    ideal  model  delta    sigma   weight residual
    1.569  1.509  0.060 2.00e-02 2.50e+03 9.01e+00
  bond pdb=" O2  PO4 C 402 "
       pdb=" P   PO4 C 402 "
    ideal  model  delta    sigma   weight residual
    1.567  1.509  0.058 2.00e-02 2.50e+03 8.43e+00
  bond pdb=" O1  PO4 C 402 "
       pdb=" P   PO4 C 402 "
    ideal  model  delta    sigma   weight residual
    1.565  1.507  0.058 2.00e-02 2.50e+03 8.39e+00
  bond pdb=" CE1 HIC C  73 "
       pdb=" NE2 HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.347  1.401 -0.054 2.00e-02 2.50e+03 7.39e+00
  ... (remaining 10381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 13748
        2.49 -     4.99: 253
        4.99 -     7.48: 18
        7.48 -     9.97: 6
        9.97 -    12.47: 3
  Bond angle restraints: 14028
  Sorted by residual:
  angle pdb=" NE  ARG A  92 "
        pdb=" CZ  ARG A  92 "
        pdb=" NH2 ARG A  92 "
      ideal   model   delta    sigma   weight residual
     119.20  114.02    5.18 9.00e-01 1.23e+00 3.32e+01
  angle pdb=" CD  ARG A  92 "
        pdb=" NE  ARG A  92 "
        pdb=" CZ  ARG A  92 "
      ideal   model   delta    sigma   weight residual
     124.40  132.11   -7.71 1.40e+00 5.10e-01 3.03e+01
  angle pdb=" C20 9UE C 404 "
        pdb=" C8  9UE C 404 "
        pdb=" C7  9UE C 404 "
      ideal   model   delta    sigma   weight residual
     118.25  105.78   12.47 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" NH1 ARG A  92 "
        pdb=" CZ  ARG A  92 "
        pdb=" NH2 ARG A  92 "
      ideal   model   delta    sigma   weight residual
     119.30  114.31    4.99 1.30e+00 5.92e-01 1.47e+01
  angle pdb=" C6  9UE C 404 "
        pdb=" N   9UE C 404 "
        pdb=" C7  9UE C 404 "
      ideal   model   delta    sigma   weight residual
     128.90  118.40   10.50 3.00e+00 1.11e-01 1.22e+01
  ... (remaining 14023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 6143
       35.87 -    71.75: 100
       71.75 -   107.62: 26
      107.62 -   143.49: 5
      143.49 -   179.36: 12
  Dihedral angle restraints: 6286
    sinusoidal: 2602
      harmonic: 3684
  Sorted by residual:
  dihedral pdb=" CD  ARG A  92 "
           pdb=" NE  ARG A  92 "
           pdb=" CZ  ARG A  92 "
           pdb=" NH1 ARG A  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   62.12  -62.12     1      1.00e+01 1.00e-02 5.11e+01
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  159.19  140.80     1      2.00e+01 2.50e-03 4.26e+01
  dihedral pdb=" CA  GLY A 563 "
           pdb=" C   GLY A 563 "
           pdb=" N   PHE A 564 "
           pdb=" CA  PHE A 564 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.13  -29.87     0      5.00e+00 4.00e-02 3.57e+01
  ... (remaining 6283 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1352
       0.081 -    0.162: 168
       0.162 -    0.242: 5
       0.242 -    0.323: 1
       0.323 -    0.404: 2
  Chirality restraints: 1528
  Sorted by residual:
  chirality pdb=" C3  9UE C 404 "
            pdb=" O   9UE C 404 "
            pdb=" C2  9UE C 404 "
            pdb=" C35 9UE C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.61   -0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" C10 9UE C 404 "
            pdb=" C18 9UE C 404 "
            pdb=" C9  9UE C 404 "
            pdb=" N2  9UE C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.38 2.00e-01 2.50e+01 3.69e+00
  chirality pdb=" C1  9UE C 404 "
            pdb=" C   9UE C 404 "
            pdb=" C15 9UE C 404 "
            pdb=" C2  9UE C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1525 not shown)

  Planarity restraints: 1797
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  92 "    0.385 9.50e-02 1.11e+02   1.99e-01 1.42e+02
        pdb=" NE  ARG A  92 "   -0.092 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  92 "    0.188 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  92 "   -0.065 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  92 "   -0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 213 "    0.316 9.50e-02 1.11e+02   1.45e-01 2.49e+01
        pdb=" NE  ARG A 213 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 213 "   -0.065 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 213 "    0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 213 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 147 "   -0.104 9.50e-02 1.11e+02   5.93e-02 1.83e+01
        pdb=" NE  ARG C 147 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 147 "   -0.070 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 147 "    0.025 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 147 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1794 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 106
        2.65 -     3.21: 9657
        3.21 -     3.77: 14999
        3.77 -     4.34: 21386
        4.34 -     4.90: 34589
  Nonbonded interactions: 80737
  Sorted by model distance:
  nonbonded pdb=" O   GLU A  71 "
            pdb=" NH2 ARG A  92 "
     model   vdw
     2.081 3.120
  nonbonded pdb=" OH  TYR A 456 "
            pdb=" OE1 GLU A 500 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" OE1 GLU B 118 "
            pdb=" NH1 ARG A 779 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" NH2 ARG B  37 "
            pdb=" O   PRO B  43 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OH  TYR A 528 "
            pdb=" O   ALA A 547 "
     model   vdw
     2.273 3.040
  ... (remaining 80732 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.660
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
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      :  0.004   0.061  10386  Z= 0.190
  Angle     :  0.841  12.467  14028  Z= 0.494
  Chirality :  0.052   0.404   1528
  Planarity :  0.010   0.199   1797
  Dihedral  : 18.219 179.363   3912
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.20), residues: 1242
  helix: -1.79 (0.16), residues: 574
  sheet:  0.22 (0.36), residues: 162
  loop : -0.20 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP C  79 
 HIS   0.014   0.002   HIS A 418 
 PHE   0.042   0.002   PHE A 671 
 TYR   0.039   0.007   TYR C 306 
 ARG   0.193   0.013   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16583 (  505)
  hydrogen bonds       : angle       7.22722 ( 1422)
  covalent geometry    : bond        0.00385 (10386)
  covalent geometry    : angle       0.84134 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9061 (m-10) cc_final: 0.8802 (m-10)
REVERT: B   93 PHE cc_start: 0.9398 (m-80) cc_final: 0.9038 (m-80)
REVERT: A  217 SER cc_start: 0.9092 (t) cc_final: 0.8486 (p)
REVERT: A  239 MET cc_start: 0.7797 (mtp) cc_final: 0.7589 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.3333
  time to fit residues: 93.1070
Evaluate side-chains
  102 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 113 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS
A  88 ASN
A 238 ASN
A 264 GLN
A 398 ASN
A 464 GLN
A 726 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.085957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.063344 restraints weight = 28572.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.065765 restraints weight = 13603.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.067412 restraints weight = 8431.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10386  Z= 0.149
  Angle     :  0.675   8.882  14028  Z= 0.354
  Chirality :  0.046   0.387   1528
  Planarity :  0.005   0.070   1797
  Dihedral  : 18.035 168.073   1430
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  6.37 %
    Favored  : 91.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.22), residues: 1242
  helix:  0.44 (0.20), residues: 593
  sheet:  0.57 (0.37), residues: 172
  loop :  0.46 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  79 
 HIS   0.011   0.002   HIS C 371 
 PHE   0.018   0.001   PHE B 144 
 TYR   0.015   0.001   TYR A 387 
 ARG   0.008   0.001   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04670 (  505)
  hydrogen bonds       : angle       5.13248 ( 1422)
  covalent geometry    : bond        0.00328 (10386)
  covalent geometry    : angle       0.67492 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9560 (m-80) cc_final: 0.9033 (m-80)
REVERT: A  296 ILE cc_start: 0.9201 (tp) cc_final: 0.8762 (tt)
REVERT: A  364 MET cc_start: 0.8909 (mmm) cc_final: 0.8671 (mmm)
REVERT: C  123 MET cc_start: 0.8577 (mmm) cc_final: 0.7812 (mmm)
REVERT: C  299 MET cc_start: 0.9131 (mmm) cc_final: 0.8780 (mmm)
  outliers start: 18
  outliers final: 9
  residues processed: 126
  average time/residue: 0.2798
  time to fit residues: 50.0174
Evaluate side-chains
  100 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  513 CYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue  236 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 7 optimal weight:   20.0000
   chunk 0 optimal weight:    9.9990
   chunk 105 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 70 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS
A 418 HIS
A 463 GLN
A 632 HIS
A 638 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.083343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.060592 restraints weight = 29515.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.062893 restraints weight = 14509.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.064428 restraints weight = 9145.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10386  Z= 0.209
  Angle     :  0.666   9.350  14028  Z= 0.342
  Chirality :  0.045   0.349   1528
  Planarity :  0.005   0.069   1797
  Dihedral  : 17.315 168.673   1430
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  7.38 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.23), residues: 1242
  helix:  1.07 (0.21), residues: 594
  sheet:  0.55 (0.39), residues: 168
  loop :  0.53 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  79 
 HIS   0.012   0.002   HIS C 371 
 PHE   0.015   0.002   PHE C 255 
 TYR   0.015   0.001   TYR A 439 
 ARG   0.005   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04474 (  505)
  hydrogen bonds       : angle       4.91894 ( 1422)
  covalent geometry    : bond        0.00472 (10386)
  covalent geometry    : angle       0.66635 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 2.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9058 (m-10) cc_final: 0.8840 (m-80)
REVERT: B   93 PHE cc_start: 0.9584 (m-80) cc_final: 0.9073 (m-80)
REVERT: B  148 ILE cc_start: 0.9531 (mm) cc_final: 0.9138 (tt)
REVERT: A   41 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7830 (ttp80)
REVERT: A  296 ILE cc_start: 0.9183 (tp) cc_final: 0.8741 (tt)
REVERT: A  364 MET cc_start: 0.8935 (mmm) cc_final: 0.8670 (mmm)
REVERT: A  467 MET cc_start: 0.8815 (ttp) cc_final: 0.8572 (ttm)
REVERT: C  299 MET cc_start: 0.9055 (mmm) cc_final: 0.8683 (mmm)
  outliers start: 24
  outliers final: 19
  residues processed: 110
  average time/residue: 0.2358
  time to fit residues: 38.7478
Evaluate side-chains
  110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 1.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  484 TRP
Chi-restraints excluded: chain A residue  503 MET
Chi-restraints excluded: chain A residue  513 CYS
Chi-restraints excluded: chain A residue  521 ASP
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  151 ILE
Chi-restraints excluded: chain C residue  285 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 78 optimal weight:    0.0030
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0970
   chunk 95 optimal weight:    0.6980
   chunk 118 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
A 420 ASN
A 775 GLN
C 121 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.085356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.062589 restraints weight = 28821.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.064946 restraints weight = 14214.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.066556 restraints weight = 8943.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10386  Z= 0.119
  Angle     :  0.608  12.172  14028  Z= 0.302
  Chirality :  0.042   0.334   1528
  Planarity :  0.004   0.047   1797
  Dihedral  : 16.488 168.578   1430
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.49 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.24), residues: 1242
  helix:  1.33 (0.21), residues: 605
  sheet:  0.48 (0.39), residues: 172
  loop :  0.57 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  79 
 HIS   0.007   0.001   HIS C 371 
 PHE   0.014   0.001   PHE B  96 
 TYR   0.013   0.001   TYR A 387 
 ARG   0.004   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  505)
  hydrogen bonds       : angle       4.63700 ( 1422)
  covalent geometry    : bond        0.00261 (10386)
  covalent geometry    : angle       0.60835 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 2.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9065 (m-10) cc_final: 0.8849 (m-80)
REVERT: B   93 PHE cc_start: 0.9567 (m-80) cc_final: 0.9063 (m-80)
REVERT: A  296 ILE cc_start: 0.9163 (tp) cc_final: 0.8770 (tt)
REVERT: A  364 MET cc_start: 0.9001 (mmm) cc_final: 0.8718 (mmm)
REVERT: A  442 GLU cc_start: 0.7841 (tt0) cc_final: 0.7435 (tt0)
REVERT: A  467 MET cc_start: 0.8762 (ttp) cc_final: 0.8543 (ttm)
REVERT: C  299 MET cc_start: 0.9038 (mmm) cc_final: 0.8777 (mtt)
  outliers start: 20
  outliers final: 13
  residues processed: 120
  average time/residue: 0.2181
  time to fit residues: 38.9556
Evaluate side-chains
  108 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  484 TRP
Chi-restraints excluded: chain A residue  503 MET
Chi-restraints excluded: chain A residue  513 CYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue  151 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 124 optimal weight:    0.0050
   chunk 41 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9980
   chunk 123 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.085407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.062396 restraints weight = 29130.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.064832 restraints weight = 13904.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.066433 restraints weight = 8641.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10386  Z= 0.121
  Angle     :  0.569   8.673  14028  Z= 0.287
  Chirality :  0.042   0.353   1528
  Planarity :  0.004   0.084   1797
  Dihedral  : 15.694 170.040   1430
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.61 %
    Favored  : 88.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.24), residues: 1242
  helix:  1.55 (0.21), residues: 605
  sheet:  0.49 (0.39), residues: 172
  loop :  0.63 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  79 
 HIS   0.006   0.001   HIS C 371 
 PHE   0.012   0.001   PHE B  96 
 TYR   0.016   0.001   TYR A 387 
 ARG   0.009   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  505)
  hydrogen bonds       : angle       4.47477 ( 1422)
  covalent geometry    : bond        0.00271 (10386)
  covalent geometry    : angle       0.56946 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 PHE cc_start: 0.9074 (m-10) cc_final: 0.8852 (m-80)
REVERT: B   93 PHE cc_start: 0.9531 (m-80) cc_final: 0.9017 (m-80)
REVERT: A  263 TYR cc_start: 0.8389 (m-80) cc_final: 0.7945 (m-10)
REVERT: A  296 ILE cc_start: 0.9126 (tp) cc_final: 0.8699 (tt)
REVERT: A  364 MET cc_start: 0.8965 (mmm) cc_final: 0.8613 (mmm)
REVERT: A  442 GLU cc_start: 0.7801 (tt0) cc_final: 0.7421 (tt0)
REVERT: A  467 MET cc_start: 0.8671 (ttp) cc_final: 0.8442 (ttm)
REVERT: A  473 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8243 (mm-30)
REVERT: C  299 MET cc_start: 0.9004 (mmm) cc_final: 0.8784 (mtt)
  outliers start: 13
  outliers final: 12
  residues processed: 111
  average time/residue: 0.2022
  time to fit residues: 33.6169
Evaluate side-chains
  106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  503 MET
Chi-restraints excluded: chain A residue  513 CYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue  370 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   chunk 3 optimal weight:    8.9990
   chunk 50 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9990
   chunk 123 optimal weight:    0.2980
   chunk 109 optimal weight:    1.9990
   chunk 121 optimal weight:    0.8980
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  42 ASN
C 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.085590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.062527 restraints weight = 29297.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.064925 restraints weight = 14358.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.066518 restraints weight = 9037.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10386  Z= 0.120
  Angle     :  0.560   8.399  14028  Z= 0.281
  Chirality :  0.041   0.304   1528
  Planarity :  0.004   0.073   1797
  Dihedral  : 15.711 172.441   1430
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.35 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.24), residues: 1242
  helix:  1.64 (0.21), residues: 607
  sheet:  0.52 (0.39), residues: 172
  loop :  0.58 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  79 
 HIS   0.006   0.001   HIS C 371 
 PHE   0.012   0.001   PHE B  96 
 TYR   0.013   0.001   TYR A 387 
 ARG   0.008   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03406 (  505)
  hydrogen bonds       : angle       4.42298 ( 1422)
  covalent geometry    : bond        0.00270 (10386)
  covalent geometry    : angle       0.55986 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 LYS cc_start: 0.9614 (tppt) cc_final: 0.9401 (tppt)
REVERT: B   36 MET cc_start: 0.8930 (tpp) cc_final: 0.8557 (tpp)
REVERT: B   93 PHE cc_start: 0.9536 (m-80) cc_final: 0.9026 (m-80)
REVERT: A  364 MET cc_start: 0.8956 (mmm) cc_final: 0.8601 (mmm)
REVERT: A  442 GLU cc_start: 0.7801 (tt0) cc_final: 0.7444 (tt0)
REVERT: A  467 MET cc_start: 0.8666 (ttp) cc_final: 0.8436 (ttm)
REVERT: C  217 CYS cc_start: 0.8243 (m) cc_final: 0.8021 (m)
  outliers start: 18
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2378
  time to fit residues: 37.6216
Evaluate side-chains
  104 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 2.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  370 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 119 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0030
   chunk 98 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0970
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
C 115 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.085981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.063080 restraints weight = 29503.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.065496 restraints weight = 14349.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.067117 restraints weight = 8989.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10386  Z= 0.112
  Angle     :  0.563   8.604  14028  Z= 0.282
  Chirality :  0.041   0.291   1528
  Planarity :  0.004   0.065   1797
  Dihedral  : 15.804 175.870   1430
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.18 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.24), residues: 1242
  helix:  1.77 (0.21), residues: 607
  sheet:  0.61 (0.39), residues: 172
  loop :  0.68 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  79 
 HIS   0.005   0.001   HIS C 371 
 PHE   0.012   0.001   PHE B  96 
 TYR   0.012   0.001   TYR A 387 
 ARG   0.007   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03299 (  505)
  hydrogen bonds       : angle       4.32309 ( 1422)
  covalent geometry    : bond        0.00255 (10386)
  covalent geometry    : angle       0.56272 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 1.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.8967 (tpp) cc_final: 0.8719 (tpp)
REVERT: B   93 PHE cc_start: 0.9541 (m-80) cc_final: 0.9054 (m-80)
REVERT: A  364 MET cc_start: 0.8985 (mmm) cc_final: 0.8640 (mmm)
REVERT: A  418 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7191 (m90)
REVERT: A  442 GLU cc_start: 0.7840 (tt0) cc_final: 0.7487 (tt0)
REVERT: A  467 MET cc_start: 0.8700 (ttp) cc_final: 0.8442 (ttm)
  outliers start: 19
  outliers final: 15
  residues processed: 113
  average time/residue: 0.2044
  time to fit residues: 35.8613
Evaluate side-chains
  110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  513 CYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  323 SER
Chi-restraints excluded: chain C residue  370 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 11 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 122 optimal weight:    0.4980
   chunk 93 optimal weight:    0.2980
   chunk 82 optimal weight:    3.9990
   chunk 94 optimal weight:    0.3980
   chunk 88 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.085902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.063077 restraints weight = 29512.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.065460 restraints weight = 14453.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.067067 restraints weight = 9076.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10386  Z= 0.110
  Angle     :  0.570   8.074  14028  Z= 0.288
  Chirality :  0.041   0.277   1528
  Planarity :  0.004   0.070   1797
  Dihedral  : 15.882 178.926   1430
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.01 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.24), residues: 1242
  helix:  1.83 (0.21), residues: 606
  sheet:  0.62 (0.38), residues: 187
  loop :  0.72 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  79 
 HIS   0.005   0.001   HIS C 371 
 PHE   0.059   0.001   PHE B  12 
 TYR   0.012   0.001   TYR A 387 
 ARG   0.011   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03255 (  505)
  hydrogen bonds       : angle       4.26448 ( 1422)
  covalent geometry    : bond        0.00250 (10386)
  covalent geometry    : angle       0.57046 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.8912 (tpp) cc_final: 0.8705 (tpp)
REVERT: B   93 PHE cc_start: 0.9535 (m-80) cc_final: 0.9051 (m-80)
REVERT: A  364 MET cc_start: 0.8973 (mmm) cc_final: 0.8597 (mmm)
REVERT: A  418 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7179 (m90)
REVERT: A  442 GLU cc_start: 0.7835 (tt0) cc_final: 0.7522 (tt0)
REVERT: A  467 MET cc_start: 0.8692 (ttp) cc_final: 0.8451 (ttm)
  outliers start: 16
  outliers final: 14
  residues processed: 111
  average time/residue: 0.2635
  time to fit residues: 45.2391
Evaluate side-chains
  112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  513 CYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  370 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 116 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0970
   chunk 70 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 50 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.085956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.062895 restraints weight = 29874.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.065294 restraints weight = 14741.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.066917 restraints weight = 9341.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10386  Z= 0.114
  Angle     :  0.568   7.750  14028  Z= 0.287
  Chirality :  0.041   0.264   1528
  Planarity :  0.004   0.061   1797
  Dihedral  : 15.892 179.149   1430
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.56 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.24), residues: 1242
  helix:  1.88 (0.22), residues: 607
  sheet:  0.45 (0.38), residues: 182
  loop :  0.72 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  79 
 HIS   0.005   0.001   HIS C 371 
 PHE   0.058   0.001   PHE B  12 
 TYR   0.011   0.001   TYR A 387 
 ARG   0.011   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03279 (  505)
  hydrogen bonds       : angle       4.23031 ( 1422)
  covalent geometry    : bond        0.00260 (10386)
  covalent geometry    : angle       0.56813 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.7694 (m-80) cc_final: 0.7019 (m-80)
REVERT: B   36 MET cc_start: 0.8854 (tpp) cc_final: 0.8634 (tpp)
REVERT: B   93 PHE cc_start: 0.9514 (m-80) cc_final: 0.8986 (m-80)
REVERT: A  299 ILE cc_start: 0.8006 (mt) cc_final: 0.7782 (tp)
REVERT: A  364 MET cc_start: 0.8952 (mmm) cc_final: 0.8555 (mmm)
REVERT: A  418 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7271 (m90)
REVERT: A  442 GLU cc_start: 0.7780 (tt0) cc_final: 0.7471 (tt0)
REVERT: A  467 MET cc_start: 0.8652 (ttp) cc_final: 0.8414 (ttm)
  outliers start: 15
  outliers final: 14
  residues processed: 113
  average time/residue: 0.2527
  time to fit residues: 43.1878
Evaluate side-chains
  114 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 2.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  513 CYS
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Chi-restraints excluded: chain C residue  370 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0770
   chunk 56 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0370
   chunk 91 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 116 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9980
   chunk 124 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.3416

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

Flipped N/Q/H residues before XYZ refinement:
A 463 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.086795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.063686 restraints weight = 29775.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.066133 restraints weight = 14677.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.067747 restraints weight = 9259.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.4452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10386  Z= 0.106
  Angle     :  0.570   7.835  14028  Z= 0.287
  Chirality :  0.041   0.250   1528
  Planarity :  0.004   0.063   1797
  Dihedral  : 15.851 178.786   1430
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.30 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.24), residues: 1242
  helix:  1.93 (0.22), residues: 606
  sheet:  0.58 (0.38), residues: 187
  loop :  0.65 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  79 
 HIS   0.005   0.001   HIS C 275 
 PHE   0.056   0.001   PHE B  12 
 TYR   0.012   0.001   TYR A 387 
 ARG   0.011   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03126 (  505)
  hydrogen bonds       : angle       4.21393 ( 1422)
  covalent geometry    : bond        0.00240 (10386)
  covalent geometry    : angle       0.57034 (14028)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.7613 (m-80) cc_final: 0.7034 (m-80)
REVERT: B   36 MET cc_start: 0.8884 (tpp) cc_final: 0.8672 (tpp)
REVERT: B   93 PHE cc_start: 0.9493 (m-80) cc_final: 0.8945 (m-80)
REVERT: A  263 TYR cc_start: 0.8381 (m-80) cc_final: 0.7847 (m-10)
REVERT: A  299 ILE cc_start: 0.7976 (mt) cc_final: 0.7735 (tp)
REVERT: A  364 MET cc_start: 0.8958 (mmm) cc_final: 0.8572 (mmm)
REVERT: A  418 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7231 (m90)
REVERT: A  442 GLU cc_start: 0.7754 (tt0) cc_final: 0.7446 (tt0)
REVERT: A  467 MET cc_start: 0.8607 (ttp) cc_final: 0.8387 (ttm)
REVERT: C  325 MET cc_start: 0.7911 (tpt) cc_final: 0.7494 (tpp)
REVERT: C  340 TRP cc_start: 0.8966 (t60) cc_final: 0.8573 (t60)
  outliers start: 13
  outliers final: 11
  residues processed: 119
  average time/residue: 0.2032
  time to fit residues: 36.1870
Evaluate side-chains
  114 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  433 ILE
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 90 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.084302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.061239 restraints weight = 29835.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.063568 restraints weight = 14774.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.065122 restraints weight = 9372.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10386  Z= 0.178
  Angle     :  0.612   7.827  14028  Z= 0.310
  Chirality :  0.043   0.253   1528
  Planarity :  0.004   0.059   1797
  Dihedral  : 15.865 178.823   1430
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.85 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.24), residues: 1242
  helix:  1.83 (0.22), residues: 609
  sheet:  0.47 (0.38), residues: 184
  loop :  0.61 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  79 
 HIS   0.006   0.001   HIS C 371 
 PHE   0.056   0.002   PHE B  12 
 TYR   0.012   0.001   TYR A 439 
 ARG   0.013   0.000   ARG B 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  505)
  hydrogen bonds       : angle       4.36740 ( 1422)
  covalent geometry    : bond        0.00409 (10386)
  covalent geometry    : angle       0.61216 (14028)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3850.18 seconds
wall clock time: 71 minutes 9.47 seconds (4269.47 seconds total)