Starting phenix.real_space_refine
on Fri Mar 14 01:33:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fzq_29637/03_2025/8fzq_29637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fzq_29637/03_2025/8fzq_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2025/8fzq_29637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2025/8fzq_29637.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2025/8fzq_29637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fzq_29637/03_2025/8fzq_29637.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 10.49, per 1000 atoms: 1.13
  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.03
  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: 3.80

  Time building geometry restraints manager: 3.28 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:             36.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     32.710
  Find NCS groups from input model:        0.090
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.890
-------------------------------------------------------------------------------
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= 0.144
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (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
 TRP   0.035   0.001   TRP A1274 
 HIS   0.002   0.001   HIS A 609 
 PHE   0.024   0.001   PHE A 587 
 TYR   0.011   0.001   TYR A 304 
 ARG   0.002   0.000   ARG A 975 

*********************** 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  : 1.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 GLN cc_start: 0.5535 (mp10) cc_final: 0.5065 (pp30)
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: 0.2187
  time to fit residues: 66.8465
Evaluate side-chains
  105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0020
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0040
   overall best weight:    0.4400

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.102926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.090126 restraints weight = 23453.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.090617 restraints weight = 20926.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091104 restraints weight = 15772.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9436  Z= 0.171
  Angle     :  0.537   7.028  12771  Z= 0.276
  Chirality :  0.040   0.178   1478
  Planarity :  0.004   0.045   1560
  Dihedral  :  8.072  84.186   1306
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.25), residues: 1121
  helix:  1.64 (0.20), residues: 738
  sheet: -0.13 (0.66), residues: 65
  loop : -1.32 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1274 
 HIS   0.002   0.001   HIS A 139 
 PHE   0.016   0.001   PHE A 131 
 TYR   0.010   0.001   TYR A 304 
 ARG   0.003   0.000   ARG A 352 

*********************** 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
  146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  525 GLN cc_start: 0.5539 (mp10) cc_final: 0.5089 (pp30)
REVERT: A 1160 VAL cc_start: 0.8491 (p) cc_final: 0.8152 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2159
  time to fit residues: 47.4006
Evaluate side-chains
  98 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0670
   chunk 50 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0470
   chunk 20 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.104166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.091279 restraints weight = 23637.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.091958 restraints weight = 17453.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.092441 restraints weight = 13195.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9436  Z= 0.160
  Angle     :  0.535   8.542  12771  Z= 0.273
  Chirality :  0.039   0.138   1478
  Planarity :  0.004   0.060   1560
  Dihedral  :  7.311  84.381   1306
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1121
  helix:  1.56 (0.19), residues: 738
  sheet: -0.09 (0.66), residues: 65
  loop : -1.34 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 202 
 HIS   0.008   0.001   HIS A 147 
 PHE   0.025   0.001   PHE A 131 
 TYR   0.013   0.001   TYR A 325 
 ARG   0.009   0.000   ARG A  75 

*********************** 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
  137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  525 GLN cc_start: 0.5460 (mt0) cc_final: 0.5073 (pp30)
REVERT: A  602 LEU cc_start: 0.8004 (tp) cc_final: 0.7511 (mp)
REVERT: A 1160 VAL cc_start: 0.8229 (p) cc_final: 0.7303 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1590
  time to fit residues: 33.8223
Evaluate side-chains
  92 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 104 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.101082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.088355 restraints weight = 23830.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.088916 restraints weight = 21434.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.089329 restraints weight = 14452.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9436  Z= 0.245
  Angle     :  0.616   7.570  12771  Z= 0.314
  Chirality :  0.042   0.239   1478
  Planarity :  0.004   0.046   1560
  Dihedral  :  6.960  85.828   1306
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.32 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1121
  helix:  1.44 (0.19), residues: 734
  sheet: -0.50 (0.60), residues: 70
  loop : -1.16 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 865 
 HIS   0.005   0.001   HIS A 147 
 PHE   0.022   0.002   PHE A 131 
 TYR   0.026   0.001   TYR A 325 
 ARG   0.007   0.001   ARG A1259 

*********************** 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
  124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 SER cc_start: 0.8826 (m) cc_final: 0.8448 (p)
REVERT: A  602 LEU cc_start: 0.8409 (tp) cc_final: 0.7776 (mp)
REVERT: A 1160 VAL cc_start: 0.8659 (p) cc_final: 0.8117 (p)
REVERT: A 1354 MET cc_start: 0.7738 (tpt) cc_final: 0.7373 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1573
  time to fit residues: 30.2529
Evaluate side-chains
  77 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 111 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 62 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 104 optimal weight:    8.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.103834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090918 restraints weight = 23819.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.091919 restraints weight = 16532.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.092493 restraints weight = 11894.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3968

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= 0.180
  Angle     :  0.547   6.982  12771  Z= 0.279
  Chirality :  0.039   0.140   1478
  Planarity :  0.004   0.046   1560
  Dihedral  :  6.723  84.894   1306
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1121
  helix:  1.61 (0.20), residues: 732
  sheet: -0.67 (0.55), residues: 80
  loop : -1.20 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A1274 
 HIS   0.006   0.001   HIS A 199 
 PHE   0.019   0.001   PHE A 131 
 TYR   0.009   0.001   TYR A 161 
 ARG   0.004   0.000   ARG A  75 

*********************** 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
  114 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 TYR cc_start: 0.7774 (t80) cc_final: 0.7424 (t80)
REVERT: A  321 SER cc_start: 0.8852 (m) cc_final: 0.8530 (p)
REVERT: A  602 LEU cc_start: 0.8453 (tp) cc_final: 0.7807 (mp)
REVERT: A 1160 VAL cc_start: 0.8616 (p) cc_final: 0.7986 (p)
REVERT: A 1282 TRP cc_start: 0.8292 (t-100) cc_final: 0.8066 (t-100)
REVERT: A 1354 MET cc_start: 0.7548 (tpt) cc_final: 0.7049 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1549
  time to fit residues: 28.1920
Evaluate side-chains
  76 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0980
   chunk 40 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3513 r_free = 0.3513 target = 0.101368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.088139 restraints weight = 23983.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.089059 restraints weight = 16344.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089471 restraints weight = 12502.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9436  Z= 0.214
  Angle     :  0.569   6.363  12771  Z= 0.293
  Chirality :  0.040   0.148   1478
  Planarity :  0.004   0.047   1560
  Dihedral  :  6.656  84.625   1306
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.82 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1121
  helix:  1.54 (0.20), residues: 733
  sheet: -0.46 (0.60), residues: 70
  loop : -1.18 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A1274 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.023   0.001   PHE A 131 
 TYR   0.015   0.001   TYR A1073 
 ARG   0.003   0.000   ARG A1102 

*********************** 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
  109 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 1.466 
Fit side-chains
REVERT: A  321 SER cc_start: 0.8842 (m) cc_final: 0.8500 (p)
REVERT: A  602 LEU cc_start: 0.8516 (tp) cc_final: 0.7867 (mp)
REVERT: A 1282 TRP cc_start: 0.8353 (t-100) cc_final: 0.8149 (t-100)
REVERT: A 1354 MET cc_start: 0.8053 (tpt) cc_final: 0.7662 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1936
  time to fit residues: 33.8629
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  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 79 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 111 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 525 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.102142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.088379 restraints weight = 24381.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.090059 restraints weight = 14484.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091169 restraints weight = 9832.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9436  Z= 0.194
  Angle     :  0.568   9.476  12771  Z= 0.286
  Chirality :  0.040   0.223   1478
  Planarity :  0.004   0.047   1560
  Dihedral  :  6.557  83.603   1306
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.21 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1121
  helix:  1.61 (0.20), residues: 730
  sheet: -0.65 (0.56), residues: 75
  loop : -1.18 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1274 
 HIS   0.023   0.001   HIS A 139 
 PHE   0.031   0.001   PHE A 131 
 TYR   0.015   0.001   TYR A1073 
 ARG   0.002   0.000   ARG A  75 

*********************** 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
  107 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  321 SER cc_start: 0.8807 (m) cc_final: 0.8480 (p)
REVERT: A  469 MET cc_start: 0.9092 (mmt) cc_final: 0.8464 (mpp)
REVERT: A  602 LEU cc_start: 0.8461 (tp) cc_final: 0.7824 (mp)
REVERT: A 1160 VAL cc_start: 0.8561 (p) cc_final: 0.8153 (p)
REVERT: A 1282 TRP cc_start: 0.8256 (t-100) cc_final: 0.8028 (t-100)
REVERT: A 1354 MET cc_start: 0.7998 (tpt) cc_final: 0.7779 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 107
  average time/residue: 0.1725
  time to fit residues: 28.1715
Evaluate side-chains
  71 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.100331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.087108 restraints weight = 24298.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.087803 restraints weight = 18128.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.088308 restraints weight = 14457.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9436  Z= 0.198
  Angle     :  0.589  13.268  12771  Z= 0.292
  Chirality :  0.040   0.197   1478
  Planarity :  0.004   0.047   1560
  Dihedral  :  6.512  82.490   1306
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1121
  helix:  1.63 (0.20), residues: 729
  sheet: -0.60 (0.57), residues: 74
  loop : -1.15 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1274 
 HIS   0.021   0.002   HIS A 139 
 PHE   0.020   0.001   PHE A 131 
 TYR   0.018   0.001   TYR A1073 
 ARG   0.002   0.000   ARG A1259 

*********************** 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
  102 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A  265 MET cc_start: 0.6998 (tpp) cc_final: 0.6636 (tpp)
REVERT: A  321 SER cc_start: 0.8763 (m) cc_final: 0.8424 (p)
REVERT: A  469 MET cc_start: 0.9149 (mmt) cc_final: 0.8544 (mpp)
REVERT: A  602 LEU cc_start: 0.8545 (tp) cc_final: 0.7868 (mp)
REVERT: A 1160 VAL cc_start: 0.8750 (p) cc_final: 0.8500 (p)
REVERT: A 1282 TRP cc_start: 0.8274 (t-100) cc_final: 0.8054 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1711
  time to fit residues: 27.4734
Evaluate side-chains
  75 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 70 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 45 optimal weight:    6.9990
   chunk 107 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.101502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.088238 restraints weight = 23817.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.088936 restraints weight = 18366.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.089343 restraints weight = 14323.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.5244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9436  Z= 0.163
  Angle     :  0.569   9.916  12771  Z= 0.284
  Chirality :  0.040   0.186   1478
  Planarity :  0.004   0.047   1560
  Dihedral  :  6.437  80.766   1306
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.25), residues: 1121
  helix:  1.69 (0.20), residues: 730
  sheet: -0.59 (0.57), residues: 75
  loop : -1.15 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1274 
 HIS   0.018   0.001   HIS A 139 
 PHE   0.036   0.001   PHE A 131 
 TYR   0.015   0.001   TYR A1073 
 ARG   0.002   0.000   ARG A1158 

*********************** 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
  110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.049 
Fit side-chains
REVERT: A  321 SER cc_start: 0.8683 (m) cc_final: 0.8409 (p)
REVERT: A  469 MET cc_start: 0.9133 (mmt) cc_final: 0.8501 (mpp)
REVERT: A  602 LEU cc_start: 0.8539 (tp) cc_final: 0.7852 (mp)
REVERT: A 1282 TRP cc_start: 0.8240 (t-100) cc_final: 0.7982 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1643
  time to fit residues: 28.1632
Evaluate side-chains
  75 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 38 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 95 optimal weight:    5.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.092290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.080146 restraints weight = 25140.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.080545 restraints weight = 20715.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.080880 restraints weight = 15935.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.6106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084   9436  Z= 0.461
  Angle     :  0.830   9.647  12771  Z= 0.422
  Chirality :  0.048   0.205   1478
  Planarity :  0.005   0.045   1560
  Dihedral  :  7.111  77.319   1306
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.24), residues: 1121
  helix:  0.81 (0.19), residues: 739
  sheet: -1.17 (0.58), residues: 69
  loop : -1.32 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1274 
 HIS   0.026   0.003   HIS A 139 
 PHE   0.038   0.003   PHE A 131 
 TYR   0.027   0.002   TYR A1032 
 ARG   0.007   0.001   ARG A  29 

********************** 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
  88 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.126 
Fit side-chains
REVERT: A  984 ASP cc_start: 0.8464 (t0) cc_final: 0.8255 (t0)
REVERT: A 1354 MET cc_start: 0.8136 (tpt) cc_final: 0.7426 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1567
  time to fit residues: 22.2891
Evaluate side-chains
  66 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 40 optimal weight:    0.1980
   chunk 82 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 88 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.097188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.084979 restraints weight = 24503.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.085570 restraints weight = 19276.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.086005 restraints weight = 13821.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.6094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9436  Z= 0.181
  Angle     :  0.598   8.759  12771  Z= 0.303
  Chirality :  0.041   0.194   1478
  Planarity :  0.004   0.046   1560
  Dihedral  :  6.586  69.267   1306
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1121
  helix:  1.41 (0.20), residues: 738
  sheet: -1.07 (0.56), residues: 80
  loop : -1.30 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A1274 
 HIS   0.017   0.001   HIS A 139 
 PHE   0.032   0.001   PHE A 131 
 TYR   0.019   0.001   TYR A1073 
 ARG   0.005   0.000   ARG A1066 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2570.39 seconds
wall clock time: 47 minutes 20.27 seconds (2840.27 seconds total)