Starting phenix.real_space_refine
on Wed Mar  4 03:09:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pm1_13509/03_2026/7pm1_13509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pm1_13509/03_2026/7pm1_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pm1_13509/03_2026/7pm1_13509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pm1_13509/03_2026/7pm1_13509.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pm1_13509/03_2026/7pm1_13509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pm1_13509/03_2026/7pm1_13509.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          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: 2.59, per 1000 atoms: 0.25
  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: 0.68
  Conformation dependent library (CDL) restraints added in 706.4 milliseconds
  

  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: 0.40
  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: 1.71

  Time building geometry restraints manager: 0.99 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:             3.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     11.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.210
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (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
 ARG   0.193   0.013   ARG A  92 
 TYR   0.039   0.007   TYR C 306 
 PHE   0.042   0.002   PHE A 671 
 TRP   0.037   0.003   TRP C  79 
 HIS   0.014   0.002   HIS A 418 

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

*********************** 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  : 0.401 
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: 0.9039 (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: 0.7590 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1079
  time to fit residues: 29.9566
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  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  42 ASN
B 147 HIS
A  88 ASN
A 238 ASN
A 264 GLN
A 398 ASN
A 464 GLN
A 632 HIS
A 638 HIS
A 726 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.084923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.062223 restraints weight = 28814.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.064613 restraints weight = 13817.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.066217 restraints weight = 8588.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.067285 restraints weight = 6198.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.067966 restraints weight = 4944.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10386  Z= 0.177
  Angle     :  0.696   8.749  14028  Z= 0.365
  Chirality :  0.047   0.421   1528
  Planarity :  0.005   0.075   1797
  Dihedral  : 17.969 168.083   1430
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  6.27 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.23), residues: 1242
  helix:  0.44 (0.20), residues: 593
  sheet:  0.51 (0.38), residues: 172
  loop :  0.39 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  37 
 TYR   0.014   0.002   TYR A 387 
 PHE   0.018   0.002   PHE B 144 
 TRP   0.017   0.002   TRP C  79 
 HIS   0.011   0.002   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (10386)
  covalent geometry    : angle       0.69569 (14028)
  hydrogen bonds       : bond        0.04635 (  505)
  hydrogen bonds       : angle       5.13697 ( 1422)

*********************** 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
  131 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9546 (m-80) cc_final: 0.9022 (m-80)
REVERT: A  217 SER cc_start: 0.9101 (t) cc_final: 0.8275 (p)
REVERT: A  296 ILE cc_start: 0.9204 (tp) cc_final: 0.8793 (tt)
REVERT: A  364 MET cc_start: 0.8828 (mmm) cc_final: 0.8567 (mmm)
REVERT: C  123 MET cc_start: 0.8572 (mmm) cc_final: 0.7813 (mmm)
REVERT: C  299 MET cc_start: 0.9123 (mmm) cc_final: 0.8765 (mmm)
  outliers start: 18
  outliers final: 10
  residues processed: 124
  average time/residue: 0.1004
  time to fit residues: 17.3568
Evaluate side-chains
  98 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
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  437 ASP
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 77 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 48 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 91 optimal weight:    0.3980
   chunk 114 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
B 147 HIS
A 418 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.085472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.062694 restraints weight = 28979.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.065122 restraints weight = 13819.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.066732 restraints weight = 8562.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.067841 restraints weight = 6175.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.068560 restraints weight = 4912.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10386  Z= 0.137
  Angle     :  0.626   9.251  14028  Z= 0.319
  Chirality :  0.043   0.315   1528
  Planarity :  0.004   0.064   1797
  Dihedral  : 17.292 168.413   1430
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  7.66 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.23), residues: 1242
  helix:  1.12 (0.21), residues: 601
  sheet:  0.56 (0.38), residues: 172
  loop :  0.57 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  92 
 TYR   0.015   0.001   TYR A 387 
 PHE   0.014   0.001   PHE B  96 
 TRP   0.010   0.001   TRP C 356 
 HIS   0.008   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10386)
  covalent geometry    : angle       0.62588 (14028)
  hydrogen bonds       : bond        0.04030 (  505)
  hydrogen bonds       : angle       4.77562 ( 1422)

*********************** 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
  127 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9571 (m-80) cc_final: 0.9056 (m-80)
REVERT: A  217 SER cc_start: 0.9131 (t) cc_final: 0.8308 (p)
REVERT: A  296 ILE cc_start: 0.9172 (tp) cc_final: 0.8747 (tt)
REVERT: A  364 MET cc_start: 0.8896 (mmm) cc_final: 0.8607 (mmm)
REVERT: A  467 MET cc_start: 0.8823 (ttp) cc_final: 0.8571 (ttm)
REVERT: C  299 MET cc_start: 0.9069 (mmm) cc_final: 0.8684 (mmm)
  outliers start: 19
  outliers final: 13
  residues processed: 119
  average time/residue: 0.0823
  time to fit residues: 14.8260
Evaluate side-chains
  103 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
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  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  119 MET
Chi-restraints excluded: chain C residue  129 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
A 420 ASN
A 463 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 = 0.3468 r_free = 0.3468 target = 0.082565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.059710 restraints weight = 29759.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.061991 restraints weight = 14664.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.063546 restraints weight = 9279.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.064594 restraints weight = 6756.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.065233 restraints weight = 5426.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10386  Z= 0.241
  Angle     :  0.676  11.812  14028  Z= 0.342
  Chirality :  0.046   0.378   1528
  Planarity :  0.004   0.051   1797
  Dihedral  : 16.604 167.991   1430
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  9.23 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.24), residues: 1242
  helix:  1.22 (0.21), residues: 600
  sheet:  0.33 (0.39), residues: 172
  loop :  0.51 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 110 
 TYR   0.018   0.002   TYR A 439 
 PHE   0.029   0.002   PHE B  12 
 TRP   0.013   0.002   TRP C  79 
 HIS   0.011   0.002   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 (10386)
  covalent geometry    : angle       0.67642 (14028)
  hydrogen bonds       : bond        0.04364 (  505)
  hydrogen bonds       : angle       4.84471 ( 1422)

*********************** 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
  118 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9587 (m-80) cc_final: 0.9083 (m-80)
REVERT: A  296 ILE cc_start: 0.9183 (tp) cc_final: 0.8790 (tt)
REVERT: A  364 MET cc_start: 0.8886 (mmm) cc_final: 0.8593 (mmm)
REVERT: A  467 MET cc_start: 0.8804 (ttp) cc_final: 0.8590 (ttm)
REVERT: C   78 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7803 (p0)
REVERT: C  299 MET cc_start: 0.9063 (mmm) cc_final: 0.8839 (mtt)
  outliers start: 24
  outliers final: 18
  residues processed: 107
  average time/residue: 0.0831
  time to fit residues: 13.4619
Evaluate side-chains
  104 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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 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  521 ASP
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  708 PHE
Chi-restraints excluded: chain C residue   78 ASN
Chi-restraints excluded: chain C residue  119 MET
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  285 CYS
Chi-restraints excluded: chain C residue  371 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0060
   chunk 90 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 122 optimal weight:    0.8980
   chunk 118 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
B  31 GLN
C 121 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.084752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.061876 restraints weight = 29344.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.064260 restraints weight = 14326.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.065845 restraints weight = 9001.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.066902 restraints weight = 6557.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.067562 restraints weight = 5274.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10386  Z= 0.123
  Angle     :  0.586  10.608  14028  Z= 0.294
  Chirality :  0.042   0.367   1528
  Planarity :  0.004   0.081   1797
  Dihedral  : 15.787 169.128   1430
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.61 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.24), residues: 1242
  helix:  1.47 (0.21), residues: 606
  sheet:  0.35 (0.39), residues: 172
  loop :  0.51 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 110 
 TYR   0.017   0.001   TYR A 387 
 PHE   0.050   0.001   PHE B  12 
 TRP   0.009   0.001   TRP C 356 
 HIS   0.009   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10386)
  covalent geometry    : angle       0.58629 (14028)
  hydrogen bonds       : bond        0.03632 (  505)
  hydrogen bonds       : angle       4.56896 ( 1422)

*********************** 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: 17
    poor density    : 101
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.8901 (tpp) cc_final: 0.8621 (tpp)
REVERT: B   93 PHE cc_start: 0.9552 (m-80) cc_final: 0.9036 (m-80)
REVERT: A  263 TYR cc_start: 0.8417 (m-80) cc_final: 0.7986 (m-10)
REVERT: A  364 MET cc_start: 0.8922 (mmm) cc_final: 0.8593 (mmm)
REVERT: A  467 MET cc_start: 0.8693 (ttp) cc_final: 0.8491 (ttm)
REVERT: A  473 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8208 (mm-30)
REVERT: C  299 MET cc_start: 0.9029 (mmm) cc_final: 0.8794 (mtt)
  outliers start: 17
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0865
  time to fit residues: 14.5419
Evaluate side-chains
  107 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 THR
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  265 LEU
Chi-restraints excluded: chain A residue  384 THR
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  236 LEU
Chi-restraints excluded: chain C residue  371 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 123 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C  78 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.084068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.061183 restraints weight = 29620.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.063537 restraints weight = 14439.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.065121 restraints weight = 9066.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.066167 restraints weight = 6606.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.066904 restraints weight = 5304.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10386  Z= 0.148
  Angle     :  0.574   8.662  14028  Z= 0.291
  Chirality :  0.042   0.311   1528
  Planarity :  0.004   0.074   1797
  Dihedral  : 15.781 171.216   1430
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.16 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.24), residues: 1242
  helix:  1.53 (0.21), residues: 607
  sheet:  0.33 (0.39), residues: 172
  loop :  0.58 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 110 
 TYR   0.013   0.001   TYR A 387 
 PHE   0.048   0.001   PHE B  12 
 TRP   0.011   0.001   TRP C  79 
 HIS   0.010   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10386)
  covalent geometry    : angle       0.57353 (14028)
  hydrogen bonds       : bond        0.03695 (  505)
  hydrogen bonds       : angle       4.51859 ( 1422)

*********************** 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
  111 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.8896 (tpp) cc_final: 0.8667 (tpp)
REVERT: B   93 PHE cc_start: 0.9549 (m-80) cc_final: 0.9043 (m-80)
REVERT: A  364 MET cc_start: 0.8914 (mmm) cc_final: 0.8589 (mmm)
REVERT: A  467 MET cc_start: 0.8706 (ttp) cc_final: 0.8489 (ttm)
REVERT: A  473 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8222 (mm-30)
REVERT: C  123 MET cc_start: 0.8227 (mmm) cc_final: 0.7883 (mmm)
  outliers start: 18
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0858
  time to fit residues: 13.8120
Evaluate side-chains
  103 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  129 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain C residue  371 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0070
   chunk 51 optimal weight:    0.8980
   chunk 112 optimal weight:    4.9990
   chunk 123 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
C  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.084885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.061952 restraints weight = 29110.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.064336 restraints weight = 14229.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.065924 restraints weight = 8927.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.067021 restraints weight = 6498.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.067781 restraints weight = 5194.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3941

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= 0.122
  Angle     :  0.563   8.753  14028  Z= 0.285
  Chirality :  0.041   0.295   1528
  Planarity :  0.004   0.062   1797
  Dihedral  : 15.894 174.988   1430
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.24), residues: 1242
  helix:  1.64 (0.21), residues: 609
  sheet:  0.48 (0.39), residues: 172
  loop :  0.53 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 110 
 TYR   0.012   0.001   TYR A 387 
 PHE   0.045   0.001   PHE B  12 
 TRP   0.010   0.001   TRP C  79 
 HIS   0.010   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10386)
  covalent geometry    : angle       0.56252 (14028)
  hydrogen bonds       : bond        0.03452 (  505)
  hydrogen bonds       : angle       4.38121 ( 1422)

*********************** 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
  116 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.8908 (tpp) cc_final: 0.8668 (tpp)
REVERT: B   93 PHE cc_start: 0.9542 (m-80) cc_final: 0.9036 (m-80)
REVERT: A  364 MET cc_start: 0.8915 (mmm) cc_final: 0.8539 (mmm)
REVERT: A  418 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7208 (m90)
REVERT: A  467 MET cc_start: 0.8695 (ttp) cc_final: 0.8464 (ttm)
  outliers start: 19
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0868
  time to fit residues: 14.3046
Evaluate side-chains
  107 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  418 HIS
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  708 PHE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain C residue  371 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0670
   chunk 105 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.7320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.084613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.061589 restraints weight = 29338.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.063967 restraints weight = 14383.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.065543 restraints weight = 9059.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.066633 restraints weight = 6604.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.067387 restraints weight = 5295.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10386  Z= 0.136
  Angle     :  0.576   8.489  14028  Z= 0.292
  Chirality :  0.042   0.281   1528
  Planarity :  0.004   0.062   1797
  Dihedral  : 15.981 177.750   1430
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.24), residues: 1242
  helix:  1.72 (0.21), residues: 609
  sheet:  0.51 (0.40), residues: 172
  loop :  0.59 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 110 
 TYR   0.011   0.001   TYR A 387 
 PHE   0.049   0.001   PHE B  12 
 TRP   0.012   0.001   TRP C  79 
 HIS   0.010   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10386)
  covalent geometry    : angle       0.57608 (14028)
  hydrogen bonds       : bond        0.03509 (  505)
  hydrogen bonds       : angle       4.36931 ( 1422)

*********************** 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
  113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.8924 (tpp) cc_final: 0.8697 (tpp)
REVERT: B   93 PHE cc_start: 0.9509 (m-80) cc_final: 0.9011 (m-80)
REVERT: A  364 MET cc_start: 0.8911 (mmm) cc_final: 0.8552 (mmm)
REVERT: A  418 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7230 (m90)
REVERT: A  467 MET cc_start: 0.8689 (ttp) cc_final: 0.8463 (ttm)
  outliers start: 16
  outliers final: 15
  residues processed: 106
  average time/residue: 0.0837
  time to fit residues: 13.5941
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  : 0.406 
-------------------------------------------------------------------------------
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  384 THR
Chi-restraints excluded: chain A residue  418 HIS
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  129 VAL
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain C residue  371 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0010
   chunk 101 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 50 optimal weight:    0.1980
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.4386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.085358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.062307 restraints weight = 29667.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.064743 restraints weight = 14562.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.066336 restraints weight = 9136.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.067392 restraints weight = 6661.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.068144 restraints weight = 5358.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10386  Z= 0.110
  Angle     :  0.562   7.926  14028  Z= 0.283
  Chirality :  0.041   0.265   1528
  Planarity :  0.004   0.058   1797
  Dihedral  : 15.983 179.567   1430
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.64 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.24), residues: 1242
  helix:  1.82 (0.21), residues: 608
  sheet:  0.52 (0.40), residues: 172
  loop :  0.58 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 110 
 TYR   0.011   0.001   TYR A 387 
 PHE   0.051   0.001   PHE B  12 
 TRP   0.011   0.001   TRP C  79 
 HIS   0.009   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10386)
  covalent geometry    : angle       0.56246 (14028)
  hydrogen bonds       : bond        0.03301 (  505)
  hydrogen bonds       : angle       4.31115 ( 1422)

*********************** 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
  120 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.7517 (m-80) cc_final: 0.7284 (m-80)
REVERT: B   36 MET cc_start: 0.8897 (tpp) cc_final: 0.8687 (tpp)
REVERT: B   93 PHE cc_start: 0.9512 (m-80) cc_final: 0.9012 (m-80)
REVERT: B  122 GLU cc_start: 0.8150 (tp30) cc_final: 0.7265 (mm-30)
REVERT: A  364 MET cc_start: 0.8909 (mmm) cc_final: 0.8552 (mmm)
REVERT: A  418 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7171 (m90)
REVERT: A  467 MET cc_start: 0.8661 (ttp) cc_final: 0.8431 (ttm)
REVERT: C  340 TRP cc_start: 0.8992 (t60) cc_final: 0.8536 (t60)
  outliers start: 17
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0883
  time to fit residues: 15.1417
Evaluate side-chains
  112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  324 THR
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain C residue  371 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 124 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 123 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 531 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.084328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061231 restraints weight = 29565.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.063598 restraints weight = 14607.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.065164 restraints weight = 9244.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.066163 restraints weight = 6768.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.066932 restraints weight = 5485.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10386  Z= 0.145
  Angle     :  0.593   8.152  14028  Z= 0.298
  Chirality :  0.042   0.259   1528
  Planarity :  0.004   0.063   1797
  Dihedral  : 15.975 179.965   1430
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.82 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.24), residues: 1242
  helix:  1.88 (0.22), residues: 606
  sheet:  0.40 (0.39), residues: 180
  loop :  0.56 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 110 
 TYR   0.012   0.001   TYR A 102 
 PHE   0.052   0.001   PHE B  12 
 TRP   0.011   0.001   TRP C  79 
 HIS   0.010   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10386)
  covalent geometry    : angle       0.59299 (14028)
  hydrogen bonds       : bond        0.03502 (  505)
  hydrogen bonds       : angle       4.35932 ( 1422)

********************** 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
  111 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.9519 (m-80) cc_final: 0.8964 (m-80)
REVERT: B  122 GLU cc_start: 0.8235 (tp30) cc_final: 0.7373 (mm-30)
REVERT: A  364 MET cc_start: 0.8907 (mmm) cc_final: 0.8551 (mmm)
REVERT: A  418 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7242 (m90)
REVERT: A  467 MET cc_start: 0.8684 (ttp) cc_final: 0.8459 (ttm)
  outliers start: 14
  outliers final: 13
  residues processed: 106
  average time/residue: 0.0935
  time to fit residues: 14.8344
Evaluate side-chains
  108 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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  384 THR
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  324 THR
Chi-restraints excluded: chain C residue  370 VAL
Chi-restraints excluded: chain C residue  371 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 102 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 97 optimal weight:    0.3980
   chunk 74 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.084573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.061504 restraints weight = 29684.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.063868 restraints weight = 14609.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.065458 restraints weight = 9225.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.066517 restraints weight = 6711.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.067262 restraints weight = 5413.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10386  Z= 0.131
  Angle     :  0.584   7.959  14028  Z= 0.293
  Chirality :  0.041   0.251   1528
  Planarity :  0.004   0.050   1797
  Dihedral  : 15.951 179.417   1430
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.47 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.24), residues: 1242
  helix:  1.89 (0.21), residues: 606
  sheet:  0.40 (0.38), residues: 184
  loop :  0.60 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 110 
 TYR   0.010   0.001   TYR A 387 
 PHE   0.053   0.001   PHE B  12 
 TRP   0.011   0.001   TRP C  79 
 HIS   0.010   0.001   HIS C 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10386)
  covalent geometry    : angle       0.58395 (14028)
  hydrogen bonds       : bond        0.03421 (  505)
  hydrogen bonds       : angle       4.34196 ( 1422)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1803.11 seconds
wall clock time: 31 minutes 50.14 seconds (1910.14 seconds total)