Starting phenix.real_space_refine
on Wed Mar  4 00:06:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fzq_29637/03_2026/8fzq_29637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fzq_29637/03_2026/8fzq_29637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2026/8fzq_29637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2026/8fzq_29637.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2026/8fzq_29637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2026/8fzq_29637.map"
  }
  resolution = 4.3
  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=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      46      5.16       5
     C    6017      2.51       5
     N    1530      2.21       5
     O    1643      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 9244
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4844
          Classifications: {'peptide': 602}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 588}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 4336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4336
          Classifications: {'peptide': 550}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 14, 'TRANS': 535}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'UNK:plan-1': 19}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 64
          Unusual residues: {' MG': 2, 'ATP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.02, per 1000 atoms: 0.22
  Number of scatterers: 9244
  At special positions: 0
  Unit cell: (108.15, 117.42, 111.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      46     16.00
     P       6     15.00
     Mg      2     11.99
     O    1643      8.00
     N    1530      7.00
     C    6017      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: 0.56
  Conformation dependent library (CDL) restraints added in 340.4 milliseconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 5 sheets defined
      71.5% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 17
    Processing helix  chain 'A' and resid 20 through 30
    Processing helix  chain 'A' and resid 41 through 44
    Processing helix  chain 'A' and resid 45 through 64
      removed outlier: 3.654A  pdb=" N   GLU A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 98
      removed outlier: 4.088A  pdb=" N   ALA A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ARG A  75 " --> pdb=" O   ASN A  71 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TRP A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ARG A  80 " --> pdb=" O   CYS A  76 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE A  81 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 110
    Processing helix  chain 'A' and resid 116 through 166
      removed outlier: 4.045A  pdb=" N   ALA A 120 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY A 126 " --> pdb=" O   TYR A 122 " (cutoff:3.500A)
      Proline residue:  A 140  - end of helix
    Processing helix  chain 'A' and resid 169 through 174
      removed outlier: 3.859A  pdb=" N   ASP A 173 " --> pdb=" O   ARG A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 198
      removed outlier: 4.046A  pdb=" N   ASN A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   LEU A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   ASN A 189 " --> pdb=" O   SER A 185 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LYS A 190 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASP A 192 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   ALA A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LEU A 197 " --> pdb=" O   GLU A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 215
      removed outlier: 4.130A  pdb=" N   ILE A 203 " --> pdb=" O   HIS A 199 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA A 204 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      Proline residue:  A 205  - end of helix
    Processing helix  chain 'A' and resid 223 through 267
      removed outlier: 4.181A  pdb=" N   LEU A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLY A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS A 254 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER A 256 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLU A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 276
    Processing helix  chain 'A' and resid 277 through 327
      removed outlier: 3.834A  pdb=" N   LYS A 294 " --> pdb=" O   GLN A 290 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LEU A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLY A 314 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   PHE A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER A 321 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      Proline residue:  A 324  - end of helix
      removed outlier: 3.624A  pdb=" N   LEU A 327 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 352
      removed outlier: 3.920A  pdb=" N   VAL A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ARG A 352 " --> pdb=" O   MET A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 376
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 463 through 473
    Processing helix  chain 'A' and resid 501 through 508
    Processing helix  chain 'A' and resid 513 through 525
    Processing helix  chain 'A' and resid 526 through 531
    Processing helix  chain 'A' and resid 549 through 564
    Processing helix  chain 'A' and resid 579 through 591
      removed outlier: 3.748A  pdb=" N   PHE A 587 " --> pdb=" O   GLU A 583 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU A 588 " --> pdb=" O   LYS A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 613
    Processing helix  chain 'A' and resid 629 through 634
    Processing helix  chain 'A' and resid 755 through 765
      removed outlier: 4.666A  pdb=" N   UNK A 761 " --> pdb=" O   UNK A 757 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   UNK A 762 " --> pdb=" O   UNK A 758 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   UNK A 765 " --> pdb=" O   UNK A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 854
      removed outlier: 3.852A  pdb=" N   TYR A 849 " --> pdb=" O   THR A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 883
      removed outlier: 3.502A  pdb=" N   ILE A 860 " --> pdb=" O   HIS A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 922
      removed outlier: 4.305A  pdb=" N   VAL A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 927
    Processing helix  chain 'A' and resid 934 through 957
    Processing helix  chain 'A' and resid 960 through 967
      removed outlier: 3.747A  pdb=" N   LEU A 967 " --> pdb=" O   THR A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 985
      removed outlier: 3.635A  pdb=" N   ARG A 975 " --> pdb=" O   GLY A 971 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   PHE A 976 " --> pdb=" O   ILE A 972 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   ILE A 980 " --> pdb=" O   PHE A 976 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ALA A 981 " --> pdb=" O   SER A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1012
      removed outlier: 4.145A  pdb=" N   LEU A 989 " --> pdb=" O   ASP A 985 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A1001 " --> pdb=" O   LEU A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1047
      removed outlier: 3.837A  pdb=" N   PHE A1016 " --> pdb=" O   GLN A1012 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL A1017 " --> pdb=" O   PRO A1013 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A1020 " --> pdb=" O   PHE A1016 " (cutoff:3.500A)
      Proline residue:  A1021  - end of helix
      removed outlier: 3.771A  pdb=" N   GLN A1035 " --> pdb=" O   ALA A1031 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   THR A1036 " --> pdb=" O   TYR A1032 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN A1039 " --> pdb=" O   GLN A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1061
      removed outlier: 3.999A  pdb=" N   PHE A1052 " --> pdb=" O   ARG A1048 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1061 through 1069
    Processing helix  chain 'A' and resid 1070 through 1121
      removed outlier: 3.523A  pdb=" N   LEU A1084 " --> pdb=" O   LYS A1080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1169
      removed outlier: 4.191A  pdb=" N   GLY A1130 " --> pdb=" O   GLU A1126 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A1139 " --> pdb=" O   LEU A1135 " (cutoff:3.500A)
      removed outlier: 5.489A  pdb=" N   MET A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   SER A1141 " --> pdb=" O   MET A1137 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   THR A1142 " --> pdb=" O   ASN A1138 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TRP A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASP A1154 " --> pdb=" O   SER A1150 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   SER A1159 " --> pdb=" O   SER A1155 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   VAL A1160 " --> pdb=" O   LEU A1156 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ARG A1162 " --> pdb=" O   ARG A1158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1249 through 1259
    Processing helix  chain 'A' and resid 1278 through 1286
      removed outlier: 3.728A  pdb=" N   PHE A1286 " --> pdb=" O   TRP A1282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1299 through 1305
    Processing helix  chain 'A' and resid 1311 through 1323
    Processing helix  chain 'A' and resid 1324 through 1331
      removed outlier: 3.965A  pdb=" N   PHE A1331 " --> pdb=" O   VAL A1327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1362
    Processing helix  chain 'A' and resid 1377 through 1392
    Processing helix  chain 'A' and resid 1404 through 1410
      removed outlier: 3.759A  pdb=" N   LEU A1408 " --> pdb=" O   GLU A1405 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A1409 " --> pdb=" O   ALA A1406 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   CYS A1410 " --> pdb=" O   MET A1407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1429 through 1434
      removed outlier: 3.793A  pdb=" N   GLU A1433 " --> pdb=" O   LYS A1429 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 394
      removed outlier: 3.665A  pdb=" N   VAL A 392 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A 446 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491
      removed outlier: 5.691A  pdb=" N   SER A 489 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   TYR A 569 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   VAL A 603 " --> pdb=" O   TYR A 569 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   LEU A 571 " --> pdb=" O   VAL A 603 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU A 453 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 8.639A  pdb=" N   LEU A 617 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ALA A 455 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   LEU A 619 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ALA A 457 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE A 616 " --> pdb=" O   TYR A 627 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   TYR A 627 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE A 618 " --> pdb=" O   TYR A 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1227 through 1230
      removed outlier: 6.097A  pdb=" N   GLU A1228 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   ALA A1217 " --> pdb=" O   GLU A1228 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A1230 " --> pdb=" O   LEU A1215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1230
      removed outlier: 6.097A  pdb=" N   GLU A1228 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   ALA A1217 " --> pdb=" O   GLU A1228 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A1230 " --> pdb=" O   LEU A1215 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU A1266 " --> pdb=" O   LYS A1213 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   LEU A1215 " --> pdb=" O   GLU A1264 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   GLU A1264 " --> pdb=" O   LEU A1215 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ALA A1217 " --> pdb=" O   ASN A1262 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   ASN A1262 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1367 through 1368
      removed outlier: 7.677A  pdb=" N   LEU A1367 " --> pdb=" O   ILE A1398 " (cutoff:3.500A)
      removed outlier: 8.664A  pdb=" N   CYS A1400 " --> pdb=" O   LEU A1367 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ARG A1239 " --> pdb=" O   GLN A1412 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   LEU A1414 " --> pdb=" O   ARG A1239 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   GLY A1241 " --> pdb=" O   LEU A1414 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   ILE A1416 " --> pdb=" O   GLY A1241 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   LEU A1243 " --> pdb=" O   ILE A1416 " (cutoff:3.500A)

    554 hydrogen bonds defined for protein.
    1644 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: 1.77

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2877
        1.34 -     1.46: 2110
        1.46 -     1.58: 4362
        1.58 -     1.69: 10
        1.69 -     1.81: 77
  Bond restraints: 9436
  Sorted by residual:
  bond pdb=" C   ALA A1081 "
       pdb=" O   ALA A1081 "
    ideal  model  delta    sigma   weight residual
    1.237  1.247 -0.010 1.19e-02 7.06e+03 7.62e-01
  bond pdb=" CA  ILE A 328 "
       pdb=" C   ILE A 328 "
    ideal  model  delta    sigma   weight residual
    1.523  1.534 -0.011 1.27e-02 6.20e+03 7.22e-01
  bond pdb=" CB  MET A 265 "
       pdb=" CG  MET A 265 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 6.68e-01
  bond pdb=" CA  HIS A 139 "
       pdb=" C   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.520  1.530 -0.010 1.23e-02 6.61e+03 6.04e-01
  bond pdb=" N   GLN A 493 "
       pdb=" CA  GLN A 493 "
    ideal  model  delta    sigma   weight residual
    1.459  1.450  0.009 1.19e-02 7.06e+03 5.94e-01
  ... (remaining 9431 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 12628
        1.96 -     3.91: 116
        3.91 -     5.87: 23
        5.87 -     7.82: 3
        7.82 -     9.78: 1
  Bond angle restraints: 12771
  Sorted by residual:
  angle pdb=" N   GLN A 493 "
        pdb=" CA  GLN A 493 "
        pdb=" C   GLN A 493 "
      ideal   model   delta    sigma   weight residual
     111.07  105.15    5.92 1.07e+00 8.73e-01 3.06e+01
  angle pdb=" C   ARG A1048 "
        pdb=" N   SER A1049 "
        pdb=" CA  SER A1049 "
      ideal   model   delta    sigma   weight residual
     120.06  123.71   -3.65 1.19e+00 7.06e-01 9.38e+00
  angle pdb=" C   THR A 388 "
        pdb=" N   THR A 389 "
        pdb=" CA  THR A 389 "
      ideal   model   delta    sigma   weight residual
     121.54  127.01   -5.47 1.91e+00 2.74e-01 8.21e+00
  angle pdb=" CA  LEU A 327 "
        pdb=" CB  LEU A 327 "
        pdb=" CG  LEU A 327 "
      ideal   model   delta    sigma   weight residual
     116.30  126.08   -9.78 3.50e+00 8.16e-02 7.81e+00
  angle pdb=" N   LEU A1335 "
        pdb=" CA  LEU A1335 "
        pdb=" CB  LEU A1335 "
      ideal   model   delta    sigma   weight residual
     113.65  109.82    3.83 1.47e+00 4.63e-01 6.79e+00
  ... (remaining 12766 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 4957
       17.67 -    35.35: 529
       35.35 -    53.02: 111
       53.02 -    70.69: 29
       70.69 -    88.37: 7
  Dihedral angle restraints: 5633
    sinusoidal: 2287
      harmonic: 3346
  Sorted by residual:
  dihedral pdb=" CA  LEU A 387 "
           pdb=" C   LEU A 387 "
           pdb=" N   THR A 388 "
           pdb=" CA  THR A 388 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.90  -18.10     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  CYS A 590 "
           pdb=" C   CYS A 590 "
           pdb=" N   VAL A 591 "
           pdb=" CA  VAL A 591 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.68  -16.32     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  CYS A  76 "
           pdb=" C   CYS A  76 "
           pdb=" N   PHE A  77 "
           pdb=" CA  PHE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.18  -15.82     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 5630 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 974
       0.032 -    0.063: 356
       0.063 -    0.095: 99
       0.095 -    0.127: 44
       0.127 -    0.159: 5
  Chirality restraints: 1478
  Sorted by residual:
  chirality pdb=" CA  GLN A 493 "
            pdb=" N   GLN A 493 "
            pdb=" C   GLN A 493 "
            pdb=" CB  GLN A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.29e-01
  chirality pdb=" CA  LEU A 323 "
            pdb=" N   LEU A 323 "
            pdb=" C   LEU A 323 "
            pdb=" CB  LEU A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE A 331 "
            pdb=" N   ILE A 331 "
            pdb=" C   ILE A 331 "
            pdb=" CB  ILE A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 1475 not shown)

  Planarity restraints: 1560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1274 "    0.017 2.00e-02 2.50e+03   1.33e-02 4.44e+00
        pdb=" CG  TRP A1274 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1274 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1274 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1274 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1274 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1274 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1274 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1274 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1049 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A1050 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A1050 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1050 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  98 "   -0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A  99 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  99 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  99 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1557 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 66
        2.58 -     3.16: 7702
        3.16 -     3.74: 14700
        3.74 -     4.32: 18177
        4.32 -     4.90: 30625
  Nonbonded interactions: 71270
  Sorted by model distance:
  nonbonded pdb="MG    MG A1502 "
            pdb=" O2B ATP A1504 "
     model   vdw
     1.999 2.170
  nonbonded pdb="MG    MG A1501 "
            pdb=" O2B ATP A1503 "
     model   vdw
     2.003 2.170
  nonbonded pdb="MG    MG A1502 "
            pdb=" O3G ATP A1504 "
     model   vdw
     2.043 2.170
  nonbonded pdb="MG    MG A1501 "
            pdb=" O3B ATP A1503 "
     model   vdw
     2.062 2.170
  nonbonded pdb=" OG  SER A1251 "
            pdb="MG    MG A1502 "
     model   vdw
     2.137 2.170
  ... (remaining 71265 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             5.120
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.900
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
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      :  0.002   0.026   9436  Z= 0.111
  Angle     :  0.529   9.779  12771  Z= 0.275
  Chirality :  0.039   0.159   1478
  Planarity :  0.003   0.044   1560
  Dihedral  : 15.435  88.368   3469
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.10 %
    Favored  : 99.80 %
  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:  1.00 (0.26), residues: 1121
  helix:  1.60 (0.20), residues: 743
  sheet: -0.26 (0.66), residues: 65
  loop : -1.42 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 975 
 TYR   0.011   0.001   TYR A 304 
 PHE   0.024   0.001   PHE A 587 
 TRP   0.035   0.001   TRP A1274 
 HIS   0.002   0.001   HIS A 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 9436)
  covalent geometry    : angle       0.52913 (12771)
  hydrogen bonds       : bond        0.11123 (  553)
  hydrogen bonds       : angle       4.66953 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1354 MET cc_start: 0.8421 (tpp) cc_final: 0.8190 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 204
  average time/residue: 0.0718
  time to fit residues: 22.3202
Evaluate side-chains
  104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 525 GLN
A 620 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.101088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.087793 restraints weight = 23959.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.088556 restraints weight = 18056.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.089070 restraints weight = 13551.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.089235 restraints weight = 11096.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.089745 restraints weight = 10482.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9436  Z= 0.169
  Angle     :  0.597   6.526  12771  Z= 0.309
  Chirality :  0.042   0.147   1478
  Planarity :  0.004   0.047   1560
  Dihedral  :  7.821  84.355   1306
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.64 %
    Favored  : 94.16 %
  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:  0.89 (0.25), residues: 1121
  helix:  1.49 (0.19), residues: 738
  sheet: -0.42 (0.63), residues: 70
  loop : -1.33 (0.31), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1158 
 TYR   0.013   0.001   TYR A1032 
 PHE   0.018   0.002   PHE A 131 
 TRP   0.021   0.001   TRP A1274 
 HIS   0.002   0.001   HIS A 949 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9436)
  covalent geometry    : angle       0.59698 (12771)
  hydrogen bonds       : bond        0.04425 (  553)
  hydrogen bonds       : angle       4.11940 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5459 (tp)
REVERT: A  452 GLN cc_start: 0.8111 (mt0) cc_final: 0.7879 (mt0)
REVERT: A  602 LEU cc_start: 0.8193 (tp) cc_final: 0.7662 (mp)
REVERT: A 1160 VAL cc_start: 0.8742 (p) cc_final: 0.8505 (p)
REVERT: A 1257 PHE cc_start: 0.8430 (m-10) cc_final: 0.8097 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0725
  time to fit residues: 15.5227
Evaluate side-chains
  92 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 61 optimal weight:   20.0000
   chunk 81 optimal weight:    0.5980
   chunk 91 optimal weight:    0.1980
   chunk 73 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 114 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 525 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.102336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.089168 restraints weight = 23905.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.089874 restraints weight = 17913.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.090271 restraints weight = 13559.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090383 restraints weight = 11626.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.091467 restraints weight = 10895.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9436  Z= 0.127
  Angle     :  0.548   8.818  12771  Z= 0.280
  Chirality :  0.039   0.168   1478
  Planarity :  0.004   0.049   1560
  Dihedral  :  7.224  84.413   1306
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.73 %
    Favored  : 95.17 %
  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:  0.92 (0.25), residues: 1121
  helix:  1.50 (0.19), residues: 742
  sheet: -0.33 (0.63), residues: 70
  loop : -1.31 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 170 
 TYR   0.014   0.001   TYR A 325 
 PHE   0.026   0.001   PHE A 131 
 TRP   0.033   0.001   TRP A 202 
 HIS   0.006   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9436)
  covalent geometry    : angle       0.54791 (12771)
  hydrogen bonds       : bond        0.04243 (  553)
  hydrogen bonds       : angle       3.95810 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  602 LEU cc_start: 0.8348 (tp) cc_final: 0.7747 (mp)
REVERT: A 1160 VAL cc_start: 0.8524 (p) cc_final: 0.8039 (p)
REVERT: A 1257 PHE cc_start: 0.8427 (m-10) cc_final: 0.8178 (m-80)
REVERT: A 1354 MET cc_start: 0.7673 (tpt) cc_final: 0.7366 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0630
  time to fit residues: 12.8144
Evaluate side-chains
  79 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0030
   chunk 38 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
A 525 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.099154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.085165 restraints weight = 24839.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.086041 restraints weight = 18523.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.086478 restraints weight = 13846.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.087077 restraints weight = 11111.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.087190 restraints weight = 10210.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.4560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   9436  Z= 0.214
  Angle     :  0.679   8.608  12771  Z= 0.348
  Chirality :  0.043   0.193   1478
  Planarity :  0.005   0.061   1560
  Dihedral  :  7.226  84.258   1306
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.43 %
    Favored  : 95.47 %
  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:  0.52 (0.25), residues: 1121
  helix:  1.16 (0.19), residues: 739
  sheet: -0.71 (0.61), residues: 70
  loop : -1.31 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A1259 
 TYR   0.019   0.002   TYR A1032 
 PHE   0.022   0.002   PHE A 131 
 TRP   0.060   0.003   TRP A1274 
 HIS   0.003   0.001   HIS A1085 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 9436)
  covalent geometry    : angle       0.67922 (12771)
  hydrogen bonds       : bond        0.05004 (  553)
  hydrogen bonds       : angle       4.31309 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  602 LEU cc_start: 0.8618 (tp) cc_final: 0.7933 (mp)
  outliers start: 1
  outliers final: 1
  residues processed: 108
  average time/residue: 0.0625
  time to fit residues: 10.9903
Evaluate side-chains
  65 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0980
   chunk 91 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 61 optimal weight:   20.0000
   chunk 46 optimal weight:    0.3980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.103008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089460 restraints weight = 24161.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.090616 restraints weight = 16745.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.091231 restraints weight = 11639.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.091846 restraints weight = 9360.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.091963 restraints weight = 8698.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9436  Z= 0.119
  Angle     :  0.542   6.732  12771  Z= 0.279
  Chirality :  0.039   0.165   1478
  Planarity :  0.004   0.048   1560
  Dihedral  :  6.726  80.722   1306
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.25), residues: 1121
  helix:  1.56 (0.20), residues: 731
  sheet: -0.54 (0.61), residues: 70
  loop : -1.25 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  75 
 TYR   0.020   0.001   TYR A 325 
 PHE   0.028   0.002   PHE A1257 
 TRP   0.030   0.001   TRP A1274 
 HIS   0.012   0.001   HIS A1079 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9436)
  covalent geometry    : angle       0.54215 (12771)
  hydrogen bonds       : bond        0.04295 (  553)
  hydrogen bonds       : angle       3.97229 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  136 LEU cc_start: 0.9047 (mt) cc_final: 0.8766 (tt)
REVERT: A  165 LEU cc_start: 0.8907 (tp) cc_final: 0.8691 (tp)
REVERT: A  304 TYR cc_start: 0.7996 (t80) cc_final: 0.7780 (t80)
REVERT: A  321 SER cc_start: 0.8825 (m) cc_final: 0.8476 (p)
REVERT: A  602 LEU cc_start: 0.8498 (tp) cc_final: 0.7844 (mp)
REVERT: A 1282 TRP cc_start: 0.8275 (t-100) cc_final: 0.7853 (t-100)
REVERT: A 1328 ILE cc_start: 0.6444 (mm) cc_final: 0.6219 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0676
  time to fit residues: 12.4084
Evaluate side-chains
  77 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 84 optimal weight:    0.5980
   chunk 38 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.101180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.087378 restraints weight = 24794.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.088413 restraints weight = 17685.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089011 restraints weight = 12390.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089608 restraints weight = 10135.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.089688 restraints weight = 9372.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9436  Z= 0.131
  Angle     :  0.547   6.918  12771  Z= 0.279
  Chirality :  0.040   0.157   1478
  Planarity :  0.004   0.048   1560
  Dihedral  :  6.598  79.256   1306
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  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:  0.94 (0.25), residues: 1121
  helix:  1.53 (0.19), residues: 738
  sheet: -0.50 (0.61), residues: 65
  loop : -1.28 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 334 
 TYR   0.013   0.001   TYR A1073 
 PHE   0.025   0.002   PHE A 131 
 TRP   0.028   0.001   TRP A1274 
 HIS   0.007   0.001   HIS A1079 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9436)
  covalent geometry    : angle       0.54667 (12771)
  hydrogen bonds       : bond        0.04199 (  553)
  hydrogen bonds       : angle       3.95228 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  136 LEU cc_start: 0.9011 (mt) cc_final: 0.8759 (tt)
REVERT: A  321 SER cc_start: 0.8753 (m) cc_final: 0.8394 (p)
REVERT: A  602 LEU cc_start: 0.8538 (tp) cc_final: 0.7834 (mp)
REVERT: A 1354 MET cc_start: 0.8736 (tpp) cc_final: 0.8435 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0680
  time to fit residues: 11.0825
Evaluate side-chains
  70 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 93 optimal weight:    7.9990
   chunk 60 optimal weight:   20.0000
   chunk 104 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 99 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.101424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.087802 restraints weight = 24602.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.088621 restraints weight = 17392.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.089061 restraints weight = 13077.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089408 restraints weight = 10976.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089564 restraints weight = 10634.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.5212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9436  Z= 0.130
  Angle     :  0.546   9.809  12771  Z= 0.281
  Chirality :  0.039   0.167   1478
  Planarity :  0.004   0.048   1560
  Dihedral  :  6.525  76.911   1306
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  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:  0.97 (0.25), residues: 1121
  helix:  1.61 (0.20), residues: 734
  sheet: -0.66 (0.57), residues: 75
  loop : -1.32 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 153 
 TYR   0.011   0.001   TYR A 304 
 PHE   0.026   0.001   PHE A 131 
 TRP   0.023   0.001   TRP A1274 
 HIS   0.007   0.001   HIS A1079 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9436)
  covalent geometry    : angle       0.54550 (12771)
  hydrogen bonds       : bond        0.04246 (  553)
  hydrogen bonds       : angle       3.93455 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  136 LEU cc_start: 0.9079 (mt) cc_final: 0.8863 (tt)
REVERT: A  265 MET cc_start: 0.6923 (tpp) cc_final: 0.6615 (tpp)
REVERT: A  321 SER cc_start: 0.8803 (m) cc_final: 0.8470 (p)
REVERT: A  602 LEU cc_start: 0.8587 (tp) cc_final: 0.7896 (mp)
REVERT: A 1160 VAL cc_start: 0.8644 (p) cc_final: 0.8042 (p)
REVERT: A 1354 MET cc_start: 0.8609 (tpp) cc_final: 0.8296 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0712
  time to fit residues: 11.8670
Evaluate side-chains
  70 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0060
   chunk 54 optimal weight:    0.2980
   overall best weight:    0.8602

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.100111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.087059 restraints weight = 23943.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.087923 restraints weight = 20869.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.088219 restraints weight = 16770.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.088700 restraints weight = 13590.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.088848 restraints weight = 11972.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9436  Z= 0.132
  Angle     :  0.555  11.199  12771  Z= 0.282
  Chirality :  0.040   0.206   1478
  Planarity :  0.004   0.048   1560
  Dihedral  :  6.434  72.150   1306
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  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:  0.97 (0.26), residues: 1121
  helix:  1.58 (0.20), residues: 736
  sheet: -0.75 (0.57), residues: 80
  loop : -1.27 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.016   0.001   TYR A1073 
 PHE   0.027   0.001   PHE A 131 
 TRP   0.024   0.001   TRP A1274 
 HIS   0.008   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9436)
  covalent geometry    : angle       0.55453 (12771)
  hydrogen bonds       : bond        0.04193 (  553)
  hydrogen bonds       : angle       3.92995 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  321 SER cc_start: 0.8771 (m) cc_final: 0.8425 (p)
REVERT: A  602 LEU cc_start: 0.8639 (tp) cc_final: 0.7958 (mp)
REVERT: A  952 MET cc_start: 0.7926 (ttm) cc_final: 0.7631 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0689
  time to fit residues: 11.1535
Evaluate side-chains
  70 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 89 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0570
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.100760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.087541 restraints weight = 24123.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.088417 restraints weight = 18549.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.088866 restraints weight = 14357.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.089727 restraints weight = 11213.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.089844 restraints weight = 9952.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.5582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9436  Z= 0.116
  Angle     :  0.552   8.822  12771  Z= 0.279
  Chirality :  0.040   0.190   1478
  Planarity :  0.004   0.048   1560
  Dihedral  :  6.322  64.636   1306
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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:  0.97 (0.26), residues: 1121
  helix:  1.62 (0.20), residues: 734
  sheet: -0.62 (0.57), residues: 80
  loop : -1.40 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 600 
 TYR   0.023   0.001   TYR A 304 
 PHE   0.028   0.001   PHE A 131 
 TRP   0.025   0.001   TRP A1274 
 HIS   0.007   0.001   HIS A1079 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9436)
  covalent geometry    : angle       0.55196 (12771)
  hydrogen bonds       : bond        0.04117 (  553)
  hydrogen bonds       : angle       3.91037 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  321 SER cc_start: 0.8743 (m) cc_final: 0.8457 (p)
REVERT: A  602 LEU cc_start: 0.8631 (tp) cc_final: 0.7923 (mp)
REVERT: A 1354 MET cc_start: 0.8121 (tpt) cc_final: 0.7835 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0703
  time to fit residues: 11.6900
Evaluate side-chains
  70 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 111 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0570
   chunk 73 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0030
   chunk 53 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.4708

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.101777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.088186 restraints weight = 24039.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089096 restraints weight = 20337.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.089744 restraints weight = 13843.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090543 restraints weight = 11206.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.090630 restraints weight = 10363.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.5668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9436  Z= 0.112
  Angle     :  0.541   8.776  12771  Z= 0.274
  Chirality :  0.039   0.187   1478
  Planarity :  0.004   0.048   1560
  Dihedral  :  6.054  59.847   1306
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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:  0.99 (0.26), residues: 1121
  helix:  1.57 (0.20), residues: 739
  sheet: -0.41 (0.58), residues: 81
  loop : -1.31 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1102 
 TYR   0.015   0.001   TYR A1073 
 PHE   0.023   0.001   PHE A 131 
 TRP   0.031   0.001   TRP A1274 
 HIS   0.009   0.001   HIS A1079 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9436)
  covalent geometry    : angle       0.54090 (12771)
  hydrogen bonds       : bond        0.04028 (  553)
  hydrogen bonds       : angle       3.89440 ( 1644)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  321 SER cc_start: 0.8647 (m) cc_final: 0.8372 (p)
REVERT: A  602 LEU cc_start: 0.8631 (tp) cc_final: 0.7932 (mp)
REVERT: A 1354 MET cc_start: 0.8080 (tpt) cc_final: 0.7803 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0789
  time to fit residues: 13.2490
Evaluate side-chains
  73 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:    0.2980
   chunk 0 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.099094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.085944 restraints weight = 24108.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.086717 restraints weight = 17460.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.086992 restraints weight = 14261.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.087126 restraints weight = 11771.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.087882 restraints weight = 10984.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.5885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9436  Z= 0.145
  Angle     :  0.582   8.890  12771  Z= 0.296
  Chirality :  0.041   0.173   1478
  Planarity :  0.004   0.047   1560
  Dihedral  :  5.917  65.102   1306
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  0.93 (0.26), residues: 1121
  helix:  1.49 (0.20), residues: 744
  sheet: -0.64 (0.57), residues: 80
  loop : -1.22 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.024   0.001   TYR A 304 
 PHE   0.021   0.001   PHE A1286 
 TRP   0.028   0.001   TRP A1274 
 HIS   0.007   0.001   HIS A1079 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9436)
  covalent geometry    : angle       0.58241 (12771)
  hydrogen bonds       : bond        0.04319 (  553)
  hydrogen bonds       : angle       4.03083 ( 1644)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1244.14 seconds
wall clock time: 22 minutes 21.74 seconds (1341.74 seconds total)