Starting phenix.real_space_refine
on Sat Jan 18 17:18:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvc_43550/01_2025/8vvc_43550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvc_43550/01_2025/8vvc_43550.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vvc_43550/01_2025/8vvc_43550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvc_43550/01_2025/8vvc_43550.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvc_43550/01_2025/8vvc_43550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvc_43550/01_2025/8vvc_43550.cif"
  }
  resolution = 4.32
  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=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1758 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    7130      2.51       5
     N    1822      2.21       5
     O    1977      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10989
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1390, 10989
          Classifications: {'peptide': 1390}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1336}
          Chain breaks: 2
  Time building chain proxies: 7.19, per 1000 atoms: 0.65
  Number of scatterers: 10989
  At special positions: 0
  Unit cell: (133.927, 129.889, 131.235, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1977      8.00
     N    1822      7.00
     C    7130      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  32 " distance=2.03

  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: 2.47
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2624

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      68.0% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 8
      removed outlier: 4.107A  pdb=" N   SER A   8 " --> pdb=" O   ARG A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 22
    Processing helix  chain 'A' and resid 30 through 58
      removed outlier: 4.247A  pdb=" N   LEU A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   VAL A  39 " --> pdb=" O   ASN A  35 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      removed outlier: 3.571A  pdb=" N   TYR A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      Proline residue:  A  51  - end of helix
    Processing helix  chain 'A' and resid 68 through 98
      removed outlier: 3.656A  pdb=" N   LYS A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 107
    Processing helix  chain 'A' and resid 108 through 131
      removed outlier: 3.921A  pdb=" N   LEU A 112 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY A 114 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 161
      removed outlier: 3.699A  pdb=" N   LEU A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 189
    Processing helix  chain 'A' and resid 208 through 212
    Processing helix  chain 'A' and resid 214 through 221
    Processing helix  chain 'A' and resid 222 through 234
      removed outlier: 3.711A  pdb=" N   GLY A 226 " --> pdb=" O   TRP A 222 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ARG A 233 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   GLN A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.717A  pdb=" N   ASP A 240 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU A 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 237 through 241'
    Processing helix  chain 'A' and resid 249 through 268
      removed outlier: 3.567A  pdb=" N   VAL A 253 " --> pdb=" O   THR A 249 " (cutoff:3.500A)
      Proline residue:  A 255  - end of helix
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.512A  pdb=" N   VAL A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 324
    Processing helix  chain 'A' and resid 325 through 355
      removed outlier: 4.130A  pdb=" N   LYS A 332 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA A 333 " --> pdb=" O   PHE A 329 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE A 334 " --> pdb=" O   PHE A 330 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET A 339 " --> pdb=" O   HIS A 335 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 340 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 359 through 410
      removed outlier: 4.269A  pdb=" N   GLY A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   TYR A 364 " --> pdb=" O   ASP A 360 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 369 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 370 " --> pdb=" O   TYR A 366 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   PHE A 371 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   GLN A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS A 386 " --> pdb=" O   HIS A 382 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE A 387 " --> pdb=" O   GLN A 383 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   TYR A 404 " --> pdb=" O   ILE A 400 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ARG A 405 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   VAL A 409 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 433
    Processing helix  chain 'A' and resid 435 through 441
    Processing helix  chain 'A' and resid 442 through 462
      removed outlier: 3.771A  pdb=" N   SER A 446 " --> pdb=" O   ASN A 442 " (cutoff:3.500A)
      Proline residue:  A 448  - end of helix
      removed outlier: 3.874A  pdb=" N   VAL A 451 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 512
      Proline residue:  A 478  - end of helix
      removed outlier: 3.510A  pdb=" N   ALA A 481 " --> pdb=" O   VAL A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 571
      removed outlier: 4.412A  pdb=" N   ALA A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      Proline residue:  A 557  - end of helix
    Processing helix  chain 'A' and resid 578 through 599
      removed outlier: 4.524A  pdb=" N   PHE A 594 " --> pdb=" O   ASN A 590 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 601 through 621
      removed outlier: 3.576A  pdb=" N   LYS A 614 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ARG A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 616 " --> pdb=" O   SER A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 692
    Processing helix  chain 'A' and resid 722 through 728
    Processing helix  chain 'A' and resid 735 through 745
    Processing helix  chain 'A' and resid 745 through 753
      removed outlier: 4.581A  pdb=" N   ASP A 749 " --> pdb=" O   ALA A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 784
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 4.252A  pdb=" N   ALA A 797 " --> pdb=" O   PRO A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 810
    Processing helix  chain 'A' and resid 852 through 859
      removed outlier: 3.824A  pdb=" N   ASP A 859 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 868
    Processing helix  chain 'A' and resid 974 through 1001
      removed outlier: 3.663A  pdb=" N   ASP A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1058
    Processing helix  chain 'A' and resid 1061 through 1066
      removed outlier: 4.446A  pdb=" N   ARG A1066 " --> pdb=" O   SER A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1085
      removed outlier: 3.687A  pdb=" N   VAL A1073 " --> pdb=" O   SER A1069 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS A1078 " --> pdb=" O   ASN A1074 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER A1085 " --> pdb=" O   ASP A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1110
      removed outlier: 3.749A  pdb=" N   MET A1093 " --> pdb=" O   GLU A1089 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1117
      removed outlier: 3.785A  pdb=" N   ALA A1116 " --> pdb=" O   PRO A1113 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A1117 " --> pdb=" O   ILE A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1161
      removed outlier: 3.830A  pdb=" N   LEU A1122 " --> pdb=" O   ILE A1118 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ARG A1138 " --> pdb=" O   VAL A1134 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   GLN A1139 " --> pdb=" O   ALA A1135 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A1140 " --> pdb=" O   SER A1136 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A1143 " --> pdb=" O   GLN A1139 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU A1144 " --> pdb=" O   LEU A1140 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   SER A1145 " --> pdb=" O   LYS A1141 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER A1149 " --> pdb=" O   SER A1145 " (cutoff:3.500A)
      Proline residue:  A1150  - end of helix
    Processing helix  chain 'A' and resid 1161 through 1168
    Processing helix  chain 'A' and resid 1171 through 1220
      removed outlier: 3.890A  pdb=" N   ALA A1188 " --> pdb=" O   GLU A1184 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR A1189 " --> pdb=" O   ASN A1185 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A1190 " --> pdb=" O   GLN A1186 " (cutoff:3.500A)
      Proline residue:  A1191  - end of helix
      removed outlier: 3.814A  pdb=" N   VAL A1194 " --> pdb=" O   TYR A1190 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ALA A1195 " --> pdb=" O   PRO A1191 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA A1200 " --> pdb=" O   ASN A1196 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   CYS A1205 " --> pdb=" O   VAL A1201 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   VAL A1206 " --> pdb=" O   ARG A1202 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A1207 " --> pdb=" O   LEU A1203 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A1218 " --> pdb=" O   ALA A1214 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1225
      removed outlier: 3.505A  pdb=" N   SER A1224 " --> pdb=" O   SER A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1254
      removed outlier: 3.564A  pdb=" N   VAL A1230 " --> pdb=" O   SER A1226 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER A1237 " --> pdb=" O   SER A1233 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU A1238 " --> pdb=" O   VAL A1234 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLN A1239 " --> pdb=" O   SER A1235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1254 through 1268
    Processing helix  chain 'A' and resid 1332 through 1342
      removed outlier: 3.578A  pdb=" N   ARG A1342 " --> pdb=" O   LEU A1338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1362 through 1368
    Processing helix  chain 'A' and resid 1384 through 1388
    Processing helix  chain 'A' and resid 1395 through 1406
      removed outlier: 3.662A  pdb=" N   VAL A1399 " --> pdb=" O   SER A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1409 through 1415
    Processing helix  chain 'A' and resid 1417 through 1420
    Processing helix  chain 'A' and resid 1424 through 1428
      removed outlier: 3.513A  pdb=" N   GLU A1428 " --> pdb=" O   GLU A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1431 through 1447
      removed outlier: 3.706A  pdb=" N   ARG A1435 " --> pdb=" O   SER A1431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1461 through 1477
    Processing helix  chain 'A' and resid 1510 through 1517
    Processing helix  chain 'A' and resid 1519 through 1528
      removed outlier: 3.617A  pdb=" N   ALA A1528 " --> pdb=" O   MET A1524 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 669
      removed outlier: 6.565A  pdb=" N   ASN A 662 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   THR A 650 " --> pdb=" O   ASN A 662 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   ILE A 664 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ALA A 649 " --> pdb=" O   GLU A 699 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   GLU A 699 " --> pdb=" O   ALA A 649 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   PHE A 651 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   LYS A 697 " --> pdb=" O   PHE A 651 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711
      removed outlier: 6.370A  pdb=" N   ALA A 709 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ASP A 792 " --> pdb=" O   ALA A 709 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   VAL A 711 " --> pdb=" O   ASP A 792 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   TYR A 789 " --> pdb=" O   ILE A 823 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   VAL A 825 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   PHE A 791 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 824 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 837 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   ILE A 839 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ALA A 675 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   MET A 841 " --> pdb=" O   ALA A 675 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL A 677 " --> pdb=" O   MET A 841 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   ILE A 838 " --> pdb=" O   MET A 849 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   MET A 849 " --> pdb=" O   ILE A 838 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   VAL A 840 " --> pdb=" O   SER A 847 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 720 through 721
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1295 through 1298
      removed outlier: 5.363A  pdb=" N   ILE A1313 " --> pdb=" O   ASN A1297 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 5.337A  pdb=" N   GLY A1324 " --> pdb=" O   ILE A1498 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   LEU A1500 " --> pdb=" O   GLY A1324 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL A1326 " --> pdb=" O   LEU A1500 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   VAL A1497 " --> pdb=" O   TYR A1508 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   TYR A1508 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   VAL A1499 " --> pdb=" O   GLN A1506 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1352 through 1353
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1371 through 1372
      removed outlier: 3.655A  pdb=" N   THR A1371 " --> pdb=" O   ILE A1450 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1382 through 1383

    642 hydrogen bonds defined for protein.
    1878 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: 3.97

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1854
        1.32 -     1.45: 2939
        1.45 -     1.57: 6349
        1.57 -     1.70: 0
        1.70 -     1.82: 95
  Bond restraints: 11237
  Sorted by residual:
  bond pdb=" N   VAL A 477 "
       pdb=" CA  VAL A 477 "
    ideal  model  delta    sigma   weight residual
    1.461  1.503 -0.042 1.23e-02 6.61e+03 1.14e+01
  bond pdb=" C   VAL A 466 "
       pdb=" O   VAL A 466 "
    ideal  model  delta    sigma   weight residual
    1.238  1.198  0.039 1.32e-02 5.74e+03 8.78e+00
  bond pdb=" N   ILE A 100 "
       pdb=" CA  ILE A 100 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.10e-02 8.26e+03 8.74e+00
  bond pdb=" N   VAL A 472 "
       pdb=" CA  VAL A 472 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.10e+00
  bond pdb=" N   VAL A 105 "
       pdb=" CA  VAL A 105 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 1.19e-02 7.06e+03 6.80e+00
  ... (remaining 11232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 14819
        1.90 -     3.81: 345
        3.81 -     5.71: 76
        5.71 -     7.61: 19
        7.61 -     9.52: 5
  Bond angle restraints: 15264
  Sorted by residual:
  angle pdb=" N   LEU A 467 "
        pdb=" CA  LEU A 467 "
        pdb=" C   LEU A 467 "
      ideal   model   delta    sigma   weight residual
     112.23  104.72    7.51 1.26e+00 6.30e-01 3.55e+01
  angle pdb=" C   LYS A1418 "
        pdb=" CA  LYS A1418 "
        pdb=" CB  LYS A1418 "
      ideal   model   delta    sigma   weight residual
     117.23  110.11    7.12 1.36e+00 5.41e-01 2.74e+01
  angle pdb=" N   VAL A 466 "
        pdb=" CA  VAL A 466 "
        pdb=" C   VAL A 466 "
      ideal   model   delta    sigma   weight residual
     113.07  106.55    6.52 1.36e+00 5.41e-01 2.30e+01
  angle pdb=" N   VAL A 470 "
        pdb=" CA  VAL A 470 "
        pdb=" C   VAL A 470 "
      ideal   model   delta    sigma   weight residual
     110.72  105.93    4.79 1.01e+00 9.80e-01 2.25e+01
  angle pdb=" N   ALA A 468 "
        pdb=" CA  ALA A 468 "
        pdb=" C   ALA A 468 "
      ideal   model   delta    sigma   weight residual
     111.82  106.34    5.48 1.16e+00 7.43e-01 2.23e+01
  ... (remaining 15259 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6072
       17.99 -    35.98: 487
       35.98 -    53.97: 102
       53.97 -    71.96: 14
       71.96 -    89.96: 11
  Dihedral angle restraints: 6686
    sinusoidal: 2630
      harmonic: 4056
  Sorted by residual:
  dihedral pdb=" CA  MET A1254 "
           pdb=" C   MET A1254 "
           pdb=" N   GLU A1255 "
           pdb=" CA  GLU A1255 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.83   28.17     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  ILE A  65 "
           pdb=" C   ILE A  65 "
           pdb=" N   GLN A  66 "
           pdb=" CA  GLN A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  LYS A 246 "
           pdb=" C   LYS A 246 "
           pdb=" N   GLU A 247 "
           pdb=" CA  GLU A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.01   19.99     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 6683 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1396
       0.051 -    0.103: 316
       0.103 -    0.154: 49
       0.154 -    0.205: 10
       0.205 -    0.257: 3
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CA  VAL A 470 "
            pdb=" N   VAL A 470 "
            pdb=" C   VAL A 470 "
            pdb=" CB  VAL A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  ILE A1373 "
            pdb=" CA  ILE A1373 "
            pdb=" CG1 ILE A1373 "
            pdb=" CG2 ILE A1373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  VAL A 477 "
            pdb=" CA  VAL A 477 "
            pdb=" CG1 VAL A 477 "
            pdb=" CG2 VAL A 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1771 not shown)

  Planarity restraints: 1906
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1248 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   VAL A1248 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   VAL A1248 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A1249 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 500 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   ASN A 500 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASN A 500 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A 501 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 489 "    0.009 2.00e-02 2.50e+03   1.90e-02 3.60e+00
        pdb=" C   THR A 489 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   THR A 489 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 490 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1903 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 868
        2.74 -     3.28: 12305
        3.28 -     3.82: 18742
        3.82 -     4.36: 20286
        4.36 -     4.90: 33538
  Nonbonded interactions: 85739
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  68 "
            pdb=" OD1 ASN A  71 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   VAL A1248 "
            pdb=" OG  SER A1252 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER A 418 "
            pdb=" O   VAL A 420 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   VAL A 548 "
            pdb=" OG1 THR A 552 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   LEU A 317 "
            pdb=" N   GLY A 322 "
     model   vdw
     2.245 3.120
  ... (remaining 85734 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:             2.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     27.370
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
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      :  0.003   0.042  11237  Z= 0.203
  Angle     :  0.749   9.518  15264  Z= 0.416
  Chirality :  0.045   0.257   1774
  Planarity :  0.005   0.044   1906
  Dihedral  : 14.066  89.956   4059
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.73 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.33 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.65 (0.23), residues: 1384
  helix:  0.35 (0.18), residues: 843
  sheet: -0.55 (0.65), residues: 58
  loop : -1.73 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 520 
 HIS   0.007   0.001   HIS A 801 
 PHE   0.015   0.001   PHE A 583 
 TYR   0.016   0.001   TYR A1033 
 ARG   0.010   0.000   ARG A1473 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  983 MET cc_start: 0.9641 (mmp) cc_final: 0.9338 (mmp)
REVERT: A 1276 TRP cc_start: 0.8738 (m100) cc_final: 0.8506 (m100)
  outliers start: 3
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1976
  time to fit residues: 42.4389
Evaluate side-chains
  116 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 108 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 126 optimal weight:   30.0000
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 805 HIS
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1364 HIS
A1387 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.088342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.064870 restraints weight = 65986.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.066128 restraints weight = 38862.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.066865 restraints weight = 27125.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11237  Z= 0.229
  Angle     :  0.666   7.579  15264  Z= 0.348
  Chirality :  0.043   0.167   1774
  Planarity :  0.005   0.054   1906
  Dihedral  :  4.789  26.441   1499
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.43 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  5.68 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.33 (0.23), residues: 1384
  helix:  0.69 (0.18), residues: 852
  sheet: -0.96 (0.60), residues: 68
  loop : -1.77 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 553 
 HIS   0.007   0.001   HIS A1421 
 PHE   0.038   0.001   PHE A 524 
 TYR   0.055   0.002   TYR A 490 
 ARG   0.004   0.001   ARG A 775 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8674 (tpp) cc_final: 0.8380 (tpp)
REVERT: A  251 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8924 (tm-30)
REVERT: A  510 ASN cc_start: 0.8149 (m110) cc_final: 0.7902 (m110)
REVERT: A  983 MET cc_start: 0.9676 (mmp) cc_final: 0.9337 (mmp)
REVERT: A 1090 VAL cc_start: 0.9393 (t) cc_final: 0.8932 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2086
  time to fit residues: 44.4780
Evaluate side-chains
  106 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 92 optimal weight:    0.4980
   chunk 98 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 128 optimal weight:   30.0000
   chunk 100 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.088339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.064624 restraints weight = 66305.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.065706 restraints weight = 40383.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.066539 restraints weight = 28147.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11237  Z= 0.203
  Angle     :  0.647   8.885  15264  Z= 0.335
  Chirality :  0.042   0.207   1774
  Planarity :  0.004   0.042   1906
  Dihedral  :  4.764  22.827   1499
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.23 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.24 (0.23), residues: 1384
  helix:  0.76 (0.18), residues: 860
  sheet: -0.87 (0.62), residues: 68
  loop : -1.79 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.034   0.001   PHE A 524 
 TYR   0.027   0.002   TYR A1243 
 ARG   0.013   0.001   ARG A 501 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8938 (tm-30)
REVERT: A  510 ASN cc_start: 0.7989 (m110) cc_final: 0.7778 (m110)
REVERT: A  983 MET cc_start: 0.9676 (mmp) cc_final: 0.9340 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2126
  time to fit residues: 43.4874
Evaluate side-chains
  104 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 129 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 102 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
A1185 ASN
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.085817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.061634 restraints weight = 68770.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.063299 restraints weight = 45385.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.063672 restraints weight = 25602.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11237  Z= 0.309
  Angle     :  0.738   7.952  15264  Z= 0.385
  Chirality :  0.045   0.166   1774
  Planarity :  0.005   0.055   1906
  Dihedral  :  4.974  24.206   1499
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.09 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.51 (0.22), residues: 1384
  helix:  0.50 (0.17), residues: 871
  sheet: -1.20 (0.65), residues: 60
  loop : -1.80 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 716 
 HIS   0.007   0.002   HIS A1421 
 PHE   0.030   0.002   PHE A 524 
 TYR   0.023   0.002   TYR A1243 
 ARG   0.015   0.001   ARG A1473 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.9575 (tt) cc_final: 0.9280 (tt)
REVERT: A  185 GLN cc_start: 0.9619 (tp40) cc_final: 0.9112 (tm-30)
REVERT: A  400 ILE cc_start: 0.9109 (mm) cc_final: 0.8903 (mt)
REVERT: A  983 MET cc_start: 0.9705 (mmp) cc_final: 0.9366 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2067
  time to fit residues: 41.4529
Evaluate side-chains
  101 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 134 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0870
   chunk 73 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 119 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 80 optimal weight:    7.9990
   overall best weight:    2.7562

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 252 GLN
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 HIS
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.087883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.063482 restraints weight = 68373.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.064521 restraints weight = 41721.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.065377 restraints weight = 28837.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11237  Z= 0.202
  Angle     :  0.658   8.388  15264  Z= 0.340
  Chirality :  0.043   0.184   1774
  Planarity :  0.004   0.038   1906
  Dihedral  :  4.869  23.596   1499
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.23 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.97 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.23 (0.22), residues: 1384
  helix:  0.77 (0.17), residues: 864
  sheet: -1.10 (0.65), residues: 60
  loop : -1.75 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 716 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.016   0.001   PHE A 583 
 TYR   0.024   0.001   TYR A  91 
 ARG   0.008   0.000   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.8887 (m-30) cc_final: 0.8495 (m-30)
REVERT: A  182 LEU cc_start: 0.9540 (tt) cc_final: 0.9271 (tt)
REVERT: A  185 GLN cc_start: 0.9599 (tp40) cc_final: 0.9153 (tm-30)
REVERT: A  983 MET cc_start: 0.9681 (mmp) cc_final: 0.9355 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2174
  time to fit residues: 43.4566
Evaluate side-chains
  99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 37 optimal weight:    4.9990
   chunk 89 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 84 optimal weight:    9.9990
   chunk 136 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 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 = 0.3717 r_free = 0.3717 target = 0.087299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.062930 restraints weight = 67773.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.064268 restraints weight = 39310.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.065036 restraints weight = 27345.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11237  Z= 0.210
  Angle     :  0.665   9.583  15264  Z= 0.342
  Chirality :  0.043   0.192   1774
  Planarity :  0.004   0.042   1906
  Dihedral  :  4.859  23.304   1499
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.86 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.11 (0.23), residues: 1384
  helix:  0.86 (0.18), residues: 867
  sheet: -0.92 (0.62), residues: 67
  loop : -1.74 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 716 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.022   0.001   PHE A 524 
 TYR   0.023   0.002   TYR A1033 
 ARG   0.013   0.001   ARG A 633 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8657 (tpp) cc_final: 0.8417 (tpp)
REVERT: A   88 ASP cc_start: 0.8899 (m-30) cc_final: 0.8651 (m-30)
REVERT: A  182 LEU cc_start: 0.9555 (tt) cc_final: 0.9272 (tt)
REVERT: A  185 GLN cc_start: 0.9609 (tp40) cc_final: 0.9082 (tm-30)
REVERT: A  251 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: A 1057 LEU cc_start: 0.9046 (tt) cc_final: 0.8836 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2325
  time to fit residues: 45.6636
Evaluate side-chains
  99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 98 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 84 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 111 optimal weight:    9.9990
   chunk 40 optimal weight:    0.6980
   chunk 122 optimal weight:    2.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 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 = 0.3732 r_free = 0.3732 target = 0.087801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.063692 restraints weight = 68117.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.064893 restraints weight = 41160.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.065699 restraints weight = 29095.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11237  Z= 0.184
  Angle     :  0.668   9.676  15264  Z= 0.338
  Chirality :  0.043   0.208   1774
  Planarity :  0.004   0.043   1906
  Dihedral  :  4.783  23.375   1499
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.58 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.02 (0.23), residues: 1384
  helix:  0.92 (0.18), residues: 867
  sheet: -0.90 (0.63), residues: 68
  loop : -1.68 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 242 
 HIS   0.004   0.001   HIS A1421 
 PHE   0.021   0.001   PHE A 524 
 TYR   0.023   0.001   TYR A1033 
 ARG   0.007   0.000   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8579 (tpp) cc_final: 0.8278 (tpp)
REVERT: A  182 LEU cc_start: 0.9539 (tt) cc_final: 0.9235 (tt)
REVERT: A  185 GLN cc_start: 0.9603 (tp40) cc_final: 0.9086 (tm-30)
REVERT: A  983 MET cc_start: 0.9666 (mmp) cc_final: 0.9345 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2153
  time to fit residues: 42.2365
Evaluate side-chains
  99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 126 optimal weight:    8.9990
   chunk 112 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 135 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 66 optimal weight:    9.9990
   chunk 114 optimal weight:    0.7980
   overall best weight:    4.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1185 ASN
** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.085625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.061715 restraints weight = 68721.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.062919 restraints weight = 41723.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.063707 restraints weight = 29752.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11237  Z= 0.286
  Angle     :  0.727   9.125  15264  Z= 0.376
  Chirality :  0.045   0.183   1774
  Planarity :  0.004   0.045   1906
  Dihedral  :  4.986  26.304   1499
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.44 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.26 (0.22), residues: 1384
  helix:  0.74 (0.17), residues: 871
  sheet: -1.34 (0.67), residues: 55
  loop : -1.77 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 242 
 HIS   0.006   0.001   HIS A1421 
 PHE   0.024   0.002   PHE A 524 
 TYR   0.022   0.002   TYR A1033 
 ARG   0.005   0.001   ARG A 633 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  513 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8766 (mttp)
REVERT: A  524 PHE cc_start: 0.8610 (p90) cc_final: 0.8387 (p90)
REVERT: A  983 MET cc_start: 0.9688 (mmp) cc_final: 0.9312 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2296
  time to fit residues: 42.8361
Evaluate side-chains
  99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 41 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 64 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0170
   chunk 119 optimal weight:    9.9990
   overall best weight:    2.4024

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1364 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.087382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.063484 restraints weight = 68234.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.064694 restraints weight = 41112.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.065587 restraints weight = 28903.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11237  Z= 0.200
  Angle     :  0.694   9.544  15264  Z= 0.352
  Chirality :  0.044   0.226   1774
  Planarity :  0.004   0.044   1906
  Dihedral  :  4.902  24.828   1499
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.79 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.11 (0.22), residues: 1384
  helix:  0.85 (0.17), residues: 870
  sheet: -1.25 (0.68), residues: 55
  loop : -1.69 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 242 
 HIS   0.004   0.001   HIS A1421 
 PHE   0.034   0.001   PHE A 551 
 TYR   0.021   0.001   TYR A  91 
 ARG   0.005   0.000   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.9531 (tt) cc_final: 0.9261 (tt)
REVERT: A  185 GLN cc_start: 0.9632 (tp40) cc_final: 0.9054 (tm-30)
REVERT: A  490 TYR cc_start: 0.7341 (m-10) cc_final: 0.6962 (m-10)
REVERT: A  513 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8770 (mttp)
REVERT: A  524 PHE cc_start: 0.8624 (p90) cc_final: 0.8374 (p90)
REVERT: A  983 MET cc_start: 0.9675 (mmp) cc_final: 0.9321 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2147
  time to fit residues: 42.0274
Evaluate side-chains
  100 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 71 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 99 optimal weight:    6.9990
   chunk 114 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0020
   chunk 44 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 138 optimal weight:   40.0000
   overall best weight:    2.0392

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1364 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.088045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.063578 restraints weight = 68922.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.064979 restraints weight = 39639.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.065720 restraints weight = 27188.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11237  Z= 0.190
  Angle     :  0.693   9.818  15264  Z= 0.348
  Chirality :  0.043   0.206   1774
  Planarity :  0.004   0.044   1906
  Dihedral  :  4.846  24.325   1499
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.79 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  0.04 (0.23), residues: 1384
  helix:  0.95 (0.18), residues: 869
  sheet: -0.65 (0.65), residues: 65
  loop : -1.69 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 242 
 HIS   0.004   0.001   HIS A 986 
 PHE   0.029   0.001   PHE A 551 
 TYR   0.019   0.001   TYR A  91 
 ARG   0.004   0.000   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8959 (tpp) cc_final: 0.8728 (tpp)
REVERT: A  182 LEU cc_start: 0.9554 (tt) cc_final: 0.9279 (tt)
REVERT: A  185 GLN cc_start: 0.9604 (tp40) cc_final: 0.9041 (tm-30)
REVERT: A  524 PHE cc_start: 0.8680 (p90) cc_final: 0.8423 (p90)
REVERT: A  983 MET cc_start: 0.9667 (mmp) cc_final: 0.9330 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2126
  time to fit residues: 40.9224
Evaluate side-chains
  98 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 132 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 78 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 480 ASN
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1364 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.087540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.062917 restraints weight = 67992.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.064242 restraints weight = 39191.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.064999 restraints weight = 27230.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11237  Z= 0.210
  Angle     :  0.703   9.453  15264  Z= 0.355
  Chirality :  0.044   0.201   1774
  Planarity :  0.004   0.044   1906
  Dihedral  :  4.823  24.053   1499
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.58 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  0.02 (0.23), residues: 1384
  helix:  0.94 (0.18), residues: 868
  sheet: -0.75 (0.64), residues: 66
  loop : -1.67 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A  86 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.030   0.001   PHE A 551 
 TYR   0.044   0.002   TYR A1243 
 ARG   0.004   0.000   ARG A1066 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4052.49 seconds
wall clock time: 73 minutes 10.21 seconds (4390.21 seconds total)