Starting phenix.real_space_refine on Sat Jan 20 16:21:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udu_26460/01_2024/7udu_26460_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udu_26460/01_2024/7udu_26460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udu_26460/01_2024/7udu_26460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udu_26460/01_2024/7udu_26460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udu_26460/01_2024/7udu_26460_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udu_26460/01_2024/7udu_26460_updated.pdb" } resolution = 4.15 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 8 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 9944 2.51 5 N 2671 2.21 5 O 2984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15711 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5661 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 23, 'TRANS': 677} Chain breaks: 2 Chain: "E" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1187 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.73, per 1000 atoms: 0.56 Number of scatterers: 15711 At special positions: 0 Unit cell: (98.88, 174.07, 166.86, 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 100 16.00 P 8 15.00 Mg 4 11.99 O 2984 8.00 N 2671 7.00 C 9944 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 - 3.50 Amino acid : False - 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: 6.59 Conformation dependent library (CDL) restraints added in 2.8 seconds 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 15 sheets defined 46.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.954A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.627A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.556A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.040A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.506A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.954A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.627A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.556A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.040A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.507A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.953A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.627A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 258 through 261 removed outlier: 3.555A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.040A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.504A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 1211 through 1213 No H-bonds generated for 'chain 'D' and resid 1211 through 1213' Processing helix chain 'D' and resid 1219 through 1231 Processing helix chain 'D' and resid 1257 through 1262 Processing helix chain 'D' and resid 1265 through 1267 No H-bonds generated for 'chain 'D' and resid 1265 through 1267' Processing helix chain 'D' and resid 1275 through 1289 removed outlier: 3.624A pdb=" N ILE D1278 " --> pdb=" O LEU D1275 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D1282 " --> pdb=" O ALA D1279 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D1287 " --> pdb=" O ALA D1284 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA D1289 " --> pdb=" O MET D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1305 through 1319 Processing helix chain 'D' and resid 1332 through 1342 Proline residue: D1336 - end of helix removed outlier: 3.546A pdb=" N PHE D1341 " --> pdb=" O LEU D1338 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1384 removed outlier: 3.543A pdb=" N ILE D1383 " --> pdb=" O LYS D1380 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D1384 " --> pdb=" O SER D1381 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1380 through 1384' Processing helix chain 'D' and resid 1394 through 1401 Processing helix chain 'D' and resid 1405 through 1410 Processing helix chain 'D' and resid 1420 through 1425 removed outlier: 3.780A pdb=" N GLN D1424 " --> pdb=" O TYR D1420 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY D1425 " --> pdb=" O TYR D1421 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1420 through 1425' Processing helix chain 'D' and resid 1436 through 1448 Processing helix chain 'D' and resid 1453 through 1471 removed outlier: 3.589A pdb=" N ASN D1471 " --> pdb=" O LEU D1467 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1498 Processing helix chain 'D' and resid 1504 through 1511 Processing helix chain 'D' and resid 1529 through 1558 Processing helix chain 'D' and resid 1584 through 1615 Processing helix chain 'D' and resid 1617 through 1619 No H-bonds generated for 'chain 'D' and resid 1617 through 1619' Processing helix chain 'D' and resid 1628 through 1635 Processing helix chain 'D' and resid 1641 through 1650 removed outlier: 3.664A pdb=" N CYS D1650 " --> pdb=" O ASP D1646 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1666 Processing helix chain 'D' and resid 1700 through 1702 No H-bonds generated for 'chain 'D' and resid 1700 through 1702' Processing helix chain 'D' and resid 1709 through 1716 Processing helix chain 'D' and resid 1721 through 1733 Processing helix chain 'D' and resid 1754 through 1771 Processing helix chain 'D' and resid 1793 through 1803 Processing helix chain 'D' and resid 1805 through 1812 Processing helix chain 'D' and resid 1823 through 1828 Processing helix chain 'D' and resid 1847 through 1854 Processing helix chain 'D' and resid 1872 through 1910 removed outlier: 3.703A pdb=" N ARG D1910 " --> pdb=" O PHE D1906 " (cutoff:3.500A) Processing helix chain 'D' and resid 1914 through 1921 Processing helix chain 'E' and resid 28 through 41 removed outlier: 3.918A pdb=" N GLN E 32 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 100 through 108 Processing helix chain 'E' and resid 120 through 129 Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 157 through 165 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.973A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.917A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.973A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.917A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.973A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.918A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 7.989A pdb=" N VAL D1295 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D1569 " --> pdb=" O VAL D1295 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE D1297 " --> pdb=" O ALA D1569 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D1571 " --> pdb=" O ILE D1297 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY D1299 " --> pdb=" O LEU D1571 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id= O, first strand: chain 'D' and resid 1682 through 1687 627 hydrogen bonds defined for protein. 1722 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: 5.42 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3232 1.33 - 1.45: 3695 1.45 - 1.57: 8929 1.57 - 1.69: 12 1.69 - 1.82: 170 Bond restraints: 16038 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.54e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" C GLY D1256 " pdb=" N PRO D1257 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.25e-02 6.40e+03 6.03e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.413 -0.044 2.00e-02 2.50e+03 4.91e+00 ... (remaining 16033 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.61: 505 106.61 - 114.02: 9064 114.02 - 121.43: 8356 121.43 - 128.83: 3706 128.83 - 136.24: 89 Bond angle restraints: 21720 Sorted by residual: angle pdb=" C VAL D1833 " pdb=" N ALA D1834 " pdb=" CA ALA D1834 " ideal model delta sigma weight residual 122.63 133.78 -11.15 1.44e+00 4.82e-01 6.00e+01 angle pdb=" C GLY D1256 " pdb=" N PRO D1257 " pdb=" CA PRO D1257 " ideal model delta sigma weight residual 119.56 113.02 6.54 1.01e+00 9.80e-01 4.19e+01 angle pdb=" N ASN D1320 " pdb=" CA ASN D1320 " pdb=" C ASN D1320 " ideal model delta sigma weight residual 109.76 101.14 8.62 1.64e+00 3.72e-01 2.76e+01 angle pdb=" N ILE D1242 " pdb=" CA ILE D1242 " pdb=" C ILE D1242 " ideal model delta sigma weight residual 109.55 116.57 -7.02 1.38e+00 5.25e-01 2.59e+01 angle pdb=" C ILE D1239 " pdb=" CA ILE D1239 " pdb=" CB ILE D1239 " ideal model delta sigma weight residual 113.22 108.29 4.93 1.12e+00 7.97e-01 1.94e+01 ... (remaining 21715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 9084 23.36 - 46.71: 520 46.71 - 70.07: 54 70.07 - 93.42: 14 93.42 - 116.78: 4 Dihedral angle restraints: 9676 sinusoidal: 3954 harmonic: 5722 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.78 116.78 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.75 116.75 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.74 116.74 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 9673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2147 0.072 - 0.143: 248 0.143 - 0.215: 6 0.215 - 0.287: 3 0.287 - 0.359: 1 Chirality restraints: 2405 Sorted by residual: chirality pdb=" CA LEU D1837 " pdb=" N LEU D1837 " pdb=" C LEU D1837 " pdb=" CB LEU D1837 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ILE D1242 " pdb=" N ILE D1242 " pdb=" C ILE D1242 " pdb=" CB ILE D1242 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE D1297 " pdb=" CA ILE D1297 " pdb=" CG1 ILE D1297 " pdb=" CG2 ILE D1297 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2402 not shown) Planarity restraints: 2800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D1251 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C MET D1251 " -0.056 2.00e-02 2.50e+03 pdb=" O MET D1251 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE D1252 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D1318 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C ALA D1318 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA D1318 " 0.018 2.00e-02 2.50e+03 pdb=" N MET D1319 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 243 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.023 5.00e-02 4.00e+02 ... (remaining 2797 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 907 2.73 - 3.27: 16050 3.27 - 3.81: 25514 3.81 - 4.36: 29967 4.36 - 4.90: 51358 Nonbonded interactions: 123796 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.187 2.170 nonbonded pdb=" N GLU D1872 " pdb=" OE1 GLU D1872 " model vdw 2.209 2.520 nonbonded pdb=" O THR D1808 " pdb=" CG1 ILE D1811 " model vdw 2.211 3.440 ... (remaining 123791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 8.190 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: 32.860 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.620 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16038 Z= 0.237 Angle : 0.674 11.152 21720 Z= 0.372 Chirality : 0.045 0.359 2405 Planarity : 0.004 0.041 2800 Dihedral : 14.256 116.776 5992 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.53 % 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: -0.29 (0.20), residues: 1943 helix: 0.68 (0.18), residues: 926 sheet: -1.06 (0.30), residues: 288 loop : -0.81 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D1619 HIS 0.003 0.001 HIS D1905 PHE 0.018 0.001 PHE E 34 TYR 0.010 0.001 TYR D1420 ARG 0.007 0.000 ARG D1491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 649 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8121 (t70) cc_final: 0.7196 (p0) REVERT: A 34 ILE cc_start: 0.8234 (mt) cc_final: 0.7758 (tp) REVERT: A 82 MET cc_start: 0.8065 (tpt) cc_final: 0.7715 (tpp) REVERT: A 111 ASN cc_start: 0.8162 (m-40) cc_final: 0.7944 (m110) REVERT: A 128 ASN cc_start: 0.8823 (t0) cc_final: 0.8587 (t0) REVERT: A 137 GLN cc_start: 0.7962 (mt0) cc_final: 0.7681 (mp10) REVERT: A 179 ASP cc_start: 0.8512 (m-30) cc_final: 0.8094 (p0) REVERT: A 195 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8601 (pt0) REVERT: A 217 CYS cc_start: 0.8171 (m) cc_final: 0.7695 (m) REVERT: A 246 GLN cc_start: 0.6084 (tt0) cc_final: 0.5678 (mt0) REVERT: A 253 GLU cc_start: 0.7320 (mp0) cc_final: 0.6828 (pm20) REVERT: A 283 MET cc_start: 0.7023 (mmt) cc_final: 0.6691 (mmt) REVERT: A 285 CYS cc_start: 0.8352 (m) cc_final: 0.8098 (p) REVERT: A 291 LYS cc_start: 0.8983 (tptp) cc_final: 0.8610 (mmtt) REVERT: A 299 MET cc_start: 0.9280 (mmm) cc_final: 0.8456 (mmp) REVERT: A 355 MET cc_start: 0.7652 (mtt) cc_final: 0.6945 (tpp) REVERT: A 360 GLN cc_start: 0.9358 (tp40) cc_final: 0.9051 (tp-100) REVERT: B 34 ILE cc_start: 0.8335 (mt) cc_final: 0.8004 (mt) REVERT: B 78 ASN cc_start: 0.7722 (t0) cc_final: 0.6752 (t0) REVERT: B 80 ASP cc_start: 0.8723 (m-30) cc_final: 0.8350 (p0) REVERT: B 95 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6629 (tpm170) REVERT: B 96 VAL cc_start: 0.8787 (t) cc_final: 0.8582 (p) REVERT: B 107 GLU cc_start: 0.6857 (tt0) cc_final: 0.6372 (tt0) REVERT: B 111 ASN cc_start: 0.8083 (m-40) cc_final: 0.7852 (m110) REVERT: B 119 MET cc_start: 0.7695 (ttm) cc_final: 0.7358 (ttm) REVERT: B 191 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8309 (mmtt) REVERT: B 196 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7656 (mtt180) REVERT: B 198 TYR cc_start: 0.8609 (m-80) cc_final: 0.8241 (m-80) REVERT: B 214 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7448 (tm-30) REVERT: B 246 GLN cc_start: 0.8674 (tt0) cc_final: 0.8180 (tm-30) REVERT: B 256 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7062 (mtp-110) REVERT: B 279 TYR cc_start: 0.6655 (t80) cc_final: 0.6300 (t80) REVERT: B 290 ARG cc_start: 0.5614 (mtt180) cc_final: 0.5350 (mtt90) REVERT: B 299 MET cc_start: 0.7912 (mmm) cc_final: 0.7538 (mtt) REVERT: B 316 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 354 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8109 (pt0) REVERT: C 11 ASP cc_start: 0.7687 (t70) cc_final: 0.6960 (m-30) REVERT: C 80 ASP cc_start: 0.8755 (m-30) cc_final: 0.8524 (m-30) REVERT: C 82 MET cc_start: 0.7571 (tpt) cc_final: 0.7303 (tpt) REVERT: C 95 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8259 (tpm170) REVERT: C 163 VAL cc_start: 0.7446 (t) cc_final: 0.7219 (t) REVERT: C 198 TYR cc_start: 0.8541 (m-80) cc_final: 0.7421 (m-80) REVERT: C 222 ASP cc_start: 0.7993 (t0) cc_final: 0.7229 (t0) REVERT: C 288 ASP cc_start: 0.6958 (m-30) cc_final: 0.6336 (p0) REVERT: C 340 TRP cc_start: 0.6248 (t60) cc_final: 0.5710 (t60) REVERT: C 355 MET cc_start: 0.7536 (mtt) cc_final: 0.7112 (mmp) REVERT: C 370 VAL cc_start: 0.7962 (p) cc_final: 0.7608 (m) REVERT: D 1251 MET cc_start: 0.8931 (tpt) cc_final: 0.8469 (mmp) REVERT: D 1274 HIS cc_start: 0.8595 (t70) cc_final: 0.7951 (t70) REVERT: D 1326 MET cc_start: 0.6889 (ptp) cc_final: 0.6430 (mmp) REVERT: D 1341 PHE cc_start: 0.7701 (m-10) cc_final: 0.7480 (m-80) REVERT: D 1349 ASN cc_start: 0.6904 (t0) cc_final: 0.6557 (t0) REVERT: D 1389 ASN cc_start: 0.8647 (m-40) cc_final: 0.8004 (t0) REVERT: D 1392 ASN cc_start: 0.8544 (t0) cc_final: 0.7246 (t0) REVERT: D 1428 CYS cc_start: 0.7638 (m) cc_final: 0.7049 (m) REVERT: D 1520 ARG cc_start: 0.8698 (mtt90) cc_final: 0.8290 (mtt-85) REVERT: D 1607 GLU cc_start: 0.8261 (tt0) cc_final: 0.7927 (tt0) REVERT: D 1609 GLN cc_start: 0.8630 (mt0) cc_final: 0.8245 (tp-100) REVERT: D 1658 THR cc_start: 0.8464 (p) cc_final: 0.7728 (t) REVERT: D 1675 LYS cc_start: 0.8794 (tttt) cc_final: 0.7976 (ptpt) REVERT: D 1688 TYR cc_start: 0.7972 (p90) cc_final: 0.7531 (p90) REVERT: D 1692 VAL cc_start: 0.8653 (t) cc_final: 0.8270 (p) REVERT: D 1752 HIS cc_start: 0.7541 (m170) cc_final: 0.7282 (m-70) REVERT: D 1823 GLN cc_start: 0.9196 (tp40) cc_final: 0.8908 (tp-100) REVERT: D 1900 PHE cc_start: 0.9663 (t80) cc_final: 0.9217 (m-80) REVERT: D 1906 PHE cc_start: 0.9833 (m-80) cc_final: 0.9430 (m-80) REVERT: E 104 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8747 (mmm160) REVERT: E 110 PHE cc_start: 0.8214 (m-80) cc_final: 0.7410 (m-80) REVERT: E 143 TYR cc_start: 0.8934 (m-10) cc_final: 0.8182 (m-10) outliers start: 1 outliers final: 0 residues processed: 650 average time/residue: 0.3222 time to fit residues: 293.1440 Evaluate side-chains 375 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 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 59 GLN B 40 HIS C 40 HIS D1274 HIS D1320 ASN ** D1321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1471 ASN D1703 ASN ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16038 Z= 0.220 Angle : 0.648 10.422 21720 Z= 0.317 Chirality : 0.045 0.191 2405 Planarity : 0.004 0.039 2800 Dihedral : 6.938 100.811 2194 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.24 % Allowed : 4.09 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1943 helix: 0.62 (0.18), residues: 924 sheet: -0.82 (0.31), residues: 274 loop : -0.61 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D1619 HIS 0.005 0.001 HIS B 371 PHE 0.020 0.002 PHE D1341 TYR 0.017 0.002 TYR D1376 ARG 0.010 0.001 ARG D1812 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 422 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8043 (t70) cc_final: 0.7111 (p0) REVERT: A 82 MET cc_start: 0.8106 (tpt) cc_final: 0.7513 (tpp) REVERT: A 107 GLU cc_start: 0.6559 (tt0) cc_final: 0.6334 (tt0) REVERT: A 111 ASN cc_start: 0.8399 (m-40) cc_final: 0.7778 (m110) REVERT: A 128 ASN cc_start: 0.8852 (t0) cc_final: 0.8609 (t0) REVERT: A 137 GLN cc_start: 0.8227 (mt0) cc_final: 0.7855 (mp10) REVERT: A 140 LEU cc_start: 0.7633 (mm) cc_final: 0.7265 (mm) REVERT: A 179 ASP cc_start: 0.8548 (m-30) cc_final: 0.7945 (p0) REVERT: A 188 TYR cc_start: 0.7848 (t80) cc_final: 0.7397 (t80) REVERT: A 195 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8595 (pt0) REVERT: A 217 CYS cc_start: 0.8153 (m) cc_final: 0.7698 (m) REVERT: A 253 GLU cc_start: 0.7475 (mp0) cc_final: 0.7183 (pm20) REVERT: A 283 MET cc_start: 0.6838 (mmt) cc_final: 0.6576 (mmt) REVERT: A 285 CYS cc_start: 0.8412 (m) cc_final: 0.8064 (p) REVERT: A 291 LYS cc_start: 0.8994 (tptp) cc_final: 0.8520 (mmtt) REVERT: A 299 MET cc_start: 0.8554 (mmm) cc_final: 0.7634 (mmp) REVERT: A 355 MET cc_start: 0.7798 (mtt) cc_final: 0.7126 (tpp) REVERT: A 360 GLN cc_start: 0.9274 (tp40) cc_final: 0.9074 (tp-100) REVERT: A 364 GLU cc_start: 0.8738 (pt0) cc_final: 0.8374 (pt0) REVERT: B 78 ASN cc_start: 0.7775 (t0) cc_final: 0.6822 (t0) REVERT: B 80 ASP cc_start: 0.8760 (m-30) cc_final: 0.8444 (p0) REVERT: B 82 MET cc_start: 0.6893 (tpt) cc_final: 0.6551 (tpt) REVERT: B 92 ASN cc_start: 0.8536 (t0) cc_final: 0.8230 (t0) REVERT: B 95 ARG cc_start: 0.7527 (mtt180) cc_final: 0.6531 (tpm170) REVERT: B 107 GLU cc_start: 0.6828 (tt0) cc_final: 0.6616 (tt0) REVERT: B 111 ASN cc_start: 0.8181 (m-40) cc_final: 0.7820 (m110) REVERT: B 167 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7814 (mp0) REVERT: B 184 ASP cc_start: 0.8416 (t0) cc_final: 0.8208 (t0) REVERT: B 191 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8220 (mmtt) REVERT: B 198 TYR cc_start: 0.8645 (m-80) cc_final: 0.8289 (m-80) REVERT: B 214 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7764 (tm-30) REVERT: B 246 GLN cc_start: 0.8595 (tt0) cc_final: 0.8167 (tm-30) REVERT: B 267 ILE cc_start: 0.8262 (mp) cc_final: 0.8059 (mp) REVERT: B 290 ARG cc_start: 0.5718 (mtt180) cc_final: 0.5180 (mtt90) REVERT: B 294 TYR cc_start: 0.6577 (m-10) cc_final: 0.6316 (m-10) REVERT: B 316 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 354 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8448 (pm20) REVERT: C 11 ASP cc_start: 0.7853 (t70) cc_final: 0.7141 (m-30) REVERT: C 95 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8228 (tpm170) REVERT: C 111 ASN cc_start: 0.8578 (m110) cc_final: 0.8083 (m110) REVERT: C 119 MET cc_start: 0.8760 (ttm) cc_final: 0.8320 (tpp) REVERT: C 140 LEU cc_start: 0.7287 (mm) cc_final: 0.6895 (mm) REVERT: C 149 THR cc_start: 0.8199 (p) cc_final: 0.7998 (m) REVERT: C 198 TYR cc_start: 0.8461 (m-80) cc_final: 0.7129 (m-80) REVERT: C 355 MET cc_start: 0.7717 (mtt) cc_final: 0.7445 (mmp) REVERT: D 1251 MET cc_start: 0.8971 (tpt) cc_final: 0.8374 (mmp) REVERT: D 1326 MET cc_start: 0.6837 (ptp) cc_final: 0.6533 (mmp) REVERT: D 1343 ASN cc_start: 0.6563 (m-40) cc_final: 0.6290 (m110) REVERT: D 1349 ASN cc_start: 0.7167 (t0) cc_final: 0.6564 (t0) REVERT: D 1389 ASN cc_start: 0.8715 (m-40) cc_final: 0.8266 (t0) REVERT: D 1392 ASN cc_start: 0.7931 (t0) cc_final: 0.7565 (t0) REVERT: D 1520 ARG cc_start: 0.8499 (mtt90) cc_final: 0.7756 (mtm-85) REVERT: D 1552 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8567 (tt) REVERT: D 1565 THR cc_start: 0.4388 (p) cc_final: 0.3964 (p) REVERT: D 1609 GLN cc_start: 0.8693 (mt0) cc_final: 0.8334 (tp-100) REVERT: D 1626 ASP cc_start: 0.8341 (p0) cc_final: 0.8095 (p0) REVERT: D 1675 LYS cc_start: 0.8744 (tttt) cc_final: 0.8015 (ptpt) REVERT: D 1692 VAL cc_start: 0.8414 (t) cc_final: 0.7947 (p) REVERT: D 1752 HIS cc_start: 0.7463 (m170) cc_final: 0.7219 (m-70) REVERT: D 1764 ASP cc_start: 0.9195 (t70) cc_final: 0.8964 (t0) REVERT: D 1792 GLU cc_start: 0.7794 (mp0) cc_final: 0.7473 (mp0) REVERT: D 1823 GLN cc_start: 0.9174 (tp40) cc_final: 0.8917 (tp-100) REVERT: D 1870 LEU cc_start: 0.8924 (tp) cc_final: 0.8528 (tp) REVERT: D 1900 PHE cc_start: 0.9667 (t80) cc_final: 0.9275 (m-80) REVERT: D 1906 PHE cc_start: 0.9818 (m-80) cc_final: 0.9482 (m-80) REVERT: E 104 ARG cc_start: 0.9126 (mmm160) cc_final: 0.8686 (mmm160) REVERT: E 107 PHE cc_start: 0.9255 (m-10) cc_final: 0.8981 (m-10) REVERT: E 110 PHE cc_start: 0.7950 (m-80) cc_final: 0.7555 (m-80) outliers start: 4 outliers final: 0 residues processed: 425 average time/residue: 0.2736 time to fit residues: 172.6202 Evaluate side-chains 325 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 142 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 121 GLN C 87 HIS D1321 GLN ** D1409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1703 ASN D1706 GLN D1905 HIS ** D1917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16038 Z= 0.201 Angle : 0.611 7.455 21720 Z= 0.301 Chirality : 0.044 0.182 2405 Planarity : 0.004 0.038 2800 Dihedral : 6.756 93.564 2194 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.24 % Allowed : 4.09 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1943 helix: 0.58 (0.18), residues: 933 sheet: -0.72 (0.30), residues: 289 loop : -0.51 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1619 HIS 0.013 0.001 HIS D1905 PHE 0.023 0.001 PHE D1548 TYR 0.032 0.002 TYR C 294 ARG 0.005 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 397 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8084 (t70) cc_final: 0.7074 (p0) REVERT: A 78 ASN cc_start: 0.7150 (t0) cc_final: 0.6518 (t0) REVERT: A 82 MET cc_start: 0.8126 (tpt) cc_final: 0.7610 (tpp) REVERT: A 107 GLU cc_start: 0.6699 (tt0) cc_final: 0.6412 (tt0) REVERT: A 111 ASN cc_start: 0.8122 (m-40) cc_final: 0.7769 (m110) REVERT: A 128 ASN cc_start: 0.8874 (t0) cc_final: 0.8532 (t0) REVERT: A 132 MET cc_start: 0.7783 (ppp) cc_final: 0.7254 (ppp) REVERT: A 137 GLN cc_start: 0.8284 (mt0) cc_final: 0.7849 (mp10) REVERT: A 154 ASP cc_start: 0.8127 (m-30) cc_final: 0.7669 (m-30) REVERT: A 179 ASP cc_start: 0.8732 (m-30) cc_final: 0.8310 (p0) REVERT: A 195 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8637 (pt0) REVERT: A 246 GLN cc_start: 0.6299 (mt0) cc_final: 0.5985 (mt0) REVERT: A 253 GLU cc_start: 0.7442 (mp0) cc_final: 0.7039 (pm20) REVERT: A 269 MET cc_start: 0.6689 (mmm) cc_final: 0.5986 (mtp) REVERT: A 282 ILE cc_start: 0.8409 (mt) cc_final: 0.8172 (mt) REVERT: A 283 MET cc_start: 0.7181 (mmt) cc_final: 0.6954 (mmt) REVERT: A 285 CYS cc_start: 0.8409 (m) cc_final: 0.8054 (p) REVERT: A 296 ASN cc_start: 0.7827 (m-40) cc_final: 0.7518 (m-40) REVERT: A 299 MET cc_start: 0.8550 (mtt) cc_final: 0.7951 (mmp) REVERT: A 355 MET cc_start: 0.7787 (mtt) cc_final: 0.7206 (tpp) REVERT: A 360 GLN cc_start: 0.9272 (tp40) cc_final: 0.9066 (tp-100) REVERT: A 364 GLU cc_start: 0.8716 (pt0) cc_final: 0.8294 (pt0) REVERT: B 78 ASN cc_start: 0.7756 (t0) cc_final: 0.6831 (t0) REVERT: B 80 ASP cc_start: 0.8771 (m-30) cc_final: 0.8508 (p0) REVERT: B 82 MET cc_start: 0.6954 (tpt) cc_final: 0.6628 (tpt) REVERT: B 92 ASN cc_start: 0.8545 (t0) cc_final: 0.8239 (t0) REVERT: B 95 ARG cc_start: 0.7479 (mtt180) cc_final: 0.6413 (tpm170) REVERT: B 111 ASN cc_start: 0.8108 (m-40) cc_final: 0.7806 (m110) REVERT: B 176 MET cc_start: 0.6070 (mtt) cc_final: 0.5794 (mtt) REVERT: B 184 ASP cc_start: 0.8407 (t0) cc_final: 0.8154 (t0) REVERT: B 191 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8250 (mmtt) REVERT: B 198 TYR cc_start: 0.8610 (m-80) cc_final: 0.8219 (m-80) REVERT: B 214 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7869 (tm-30) REVERT: B 246 GLN cc_start: 0.8500 (tt0) cc_final: 0.8123 (tm-30) REVERT: C 11 ASP cc_start: 0.8202 (t70) cc_final: 0.7333 (m-30) REVERT: C 88 HIS cc_start: 0.8502 (t70) cc_final: 0.8295 (t-170) REVERT: C 95 ARG cc_start: 0.8827 (mtt180) cc_final: 0.8169 (tpm170) REVERT: C 111 ASN cc_start: 0.8604 (m110) cc_final: 0.8005 (m110) REVERT: C 119 MET cc_start: 0.8754 (ttm) cc_final: 0.8310 (tpp) REVERT: C 125 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 128 ASN cc_start: 0.9506 (t0) cc_final: 0.9165 (m-40) REVERT: C 137 GLN cc_start: 0.6508 (mp10) cc_final: 0.6290 (mp10) REVERT: C 140 LEU cc_start: 0.7168 (mm) cc_final: 0.6718 (mm) REVERT: C 149 THR cc_start: 0.8310 (p) cc_final: 0.8050 (m) REVERT: C 195 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8595 (mm-30) REVERT: C 198 TYR cc_start: 0.8434 (m-80) cc_final: 0.7222 (m-80) REVERT: C 355 MET cc_start: 0.7717 (mtt) cc_final: 0.7445 (mmp) REVERT: D 1211 MET cc_start: 0.8149 (mpp) cc_final: 0.7708 (mpp) REVERT: D 1251 MET cc_start: 0.8957 (tpt) cc_final: 0.8250 (mmp) REVERT: D 1316 LEU cc_start: 0.9327 (tp) cc_final: 0.9057 (pp) REVERT: D 1326 MET cc_start: 0.6839 (ptp) cc_final: 0.6537 (mmp) REVERT: D 1343 ASN cc_start: 0.6705 (m-40) cc_final: 0.6389 (m110) REVERT: D 1349 ASN cc_start: 0.7037 (t0) cc_final: 0.6633 (t0) REVERT: D 1389 ASN cc_start: 0.8743 (m-40) cc_final: 0.8369 (t0) REVERT: D 1392 ASN cc_start: 0.7978 (t0) cc_final: 0.7692 (t0) REVERT: D 1397 TYR cc_start: 0.7236 (m-80) cc_final: 0.6879 (m-80) REVERT: D 1428 CYS cc_start: 0.6944 (m) cc_final: 0.6648 (m) REVERT: D 1520 ARG cc_start: 0.8519 (mtt90) cc_final: 0.7779 (mtm-85) REVERT: D 1565 THR cc_start: 0.5005 (p) cc_final: 0.4738 (p) REVERT: D 1574 TYR cc_start: 0.5807 (m-10) cc_final: 0.5552 (m-80) REVERT: D 1609 GLN cc_start: 0.8774 (mt0) cc_final: 0.8412 (tp-100) REVERT: D 1626 ASP cc_start: 0.8417 (p0) cc_final: 0.8168 (p0) REVERT: D 1675 LYS cc_start: 0.8738 (tttt) cc_final: 0.7972 (ptpt) REVERT: D 1692 VAL cc_start: 0.8520 (t) cc_final: 0.8018 (p) REVERT: D 1752 HIS cc_start: 0.7397 (m170) cc_final: 0.6622 (m170) REVERT: D 1764 ASP cc_start: 0.9184 (t70) cc_final: 0.8876 (t0) REVERT: D 1823 GLN cc_start: 0.9187 (tp40) cc_final: 0.8910 (tp-100) REVERT: D 1870 LEU cc_start: 0.8928 (tp) cc_final: 0.8545 (tp) REVERT: D 1900 PHE cc_start: 0.9675 (t80) cc_final: 0.9309 (m-80) REVERT: D 1903 GLN cc_start: 0.9881 (OUTLIER) cc_final: 0.9621 (pm20) REVERT: D 1906 PHE cc_start: 0.9758 (m-80) cc_final: 0.9434 (m-10) REVERT: E 104 ARG cc_start: 0.9222 (mmm160) cc_final: 0.8947 (mmm160) REVERT: E 107 PHE cc_start: 0.9265 (m-10) cc_final: 0.8746 (m-10) outliers start: 4 outliers final: 0 residues processed: 401 average time/residue: 0.2806 time to fit residues: 167.9265 Evaluate side-chains 306 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 188 optimal weight: 30.0000 chunk 93 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 111 ASN B 115 ASN B 121 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1590 ASN ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1886 GLN E 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16038 Z= 0.267 Angle : 0.649 7.803 21720 Z= 0.321 Chirality : 0.045 0.206 2405 Planarity : 0.004 0.040 2800 Dihedral : 6.758 90.003 2194 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.26 % 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: -0.05 (0.20), residues: 1943 helix: 0.68 (0.18), residues: 913 sheet: -0.67 (0.30), residues: 287 loop : -0.50 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.011 0.001 HIS B 275 PHE 0.028 0.002 PHE E 117 TYR 0.025 0.002 TYR E 122 ARG 0.008 0.001 ARG D1898 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 380 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8191 (t70) cc_final: 0.7191 (p0) REVERT: A 49 GLN cc_start: 0.7225 (pt0) cc_final: 0.6743 (mt0) REVERT: A 78 ASN cc_start: 0.7168 (t0) cc_final: 0.6450 (t0) REVERT: A 107 GLU cc_start: 0.6620 (tt0) cc_final: 0.5916 (tt0) REVERT: A 111 ASN cc_start: 0.8509 (m110) cc_final: 0.8008 (m110) REVERT: A 128 ASN cc_start: 0.8997 (t0) cc_final: 0.8712 (t0) REVERT: A 137 GLN cc_start: 0.8297 (mt0) cc_final: 0.7781 (mp10) REVERT: A 151 ILE cc_start: 0.8859 (mt) cc_final: 0.8580 (mm) REVERT: A 154 ASP cc_start: 0.8197 (m-30) cc_final: 0.7817 (m-30) REVERT: A 179 ASP cc_start: 0.8801 (m-30) cc_final: 0.8357 (p0) REVERT: A 195 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8712 (pt0) REVERT: A 202 THR cc_start: 0.8698 (m) cc_final: 0.8493 (p) REVERT: A 253 GLU cc_start: 0.7650 (mp0) cc_final: 0.7191 (pm20) REVERT: A 269 MET cc_start: 0.6974 (mmm) cc_final: 0.6349 (mtp) REVERT: A 283 MET cc_start: 0.7105 (mmt) cc_final: 0.6878 (mmp) REVERT: A 285 CYS cc_start: 0.8523 (m) cc_final: 0.8215 (p) REVERT: A 299 MET cc_start: 0.8474 (mtt) cc_final: 0.7929 (mmp) REVERT: A 355 MET cc_start: 0.8090 (mtt) cc_final: 0.7601 (tpp) REVERT: A 364 GLU cc_start: 0.8666 (pt0) cc_final: 0.8237 (pt0) REVERT: B 78 ASN cc_start: 0.7870 (t0) cc_final: 0.6916 (t0) REVERT: B 80 ASP cc_start: 0.8805 (m-30) cc_final: 0.8536 (p0) REVERT: B 82 MET cc_start: 0.6855 (tpt) cc_final: 0.6519 (tpt) REVERT: B 92 ASN cc_start: 0.8537 (t0) cc_final: 0.8210 (t0) REVERT: B 95 ARG cc_start: 0.7612 (mtt180) cc_final: 0.6320 (tpm170) REVERT: B 111 ASN cc_start: 0.8207 (m-40) cc_final: 0.7942 (m110) REVERT: B 176 MET cc_start: 0.6029 (mtt) cc_final: 0.5715 (mtt) REVERT: B 184 ASP cc_start: 0.8461 (t0) cc_final: 0.8194 (m-30) REVERT: B 191 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8231 (mmtt) REVERT: B 198 TYR cc_start: 0.8604 (m-80) cc_final: 0.8341 (m-80) REVERT: B 214 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7986 (tm-30) REVERT: B 246 GLN cc_start: 0.8455 (tt0) cc_final: 0.7981 (tm-30) REVERT: C 11 ASP cc_start: 0.8177 (t70) cc_final: 0.7117 (m-30) REVERT: C 34 ILE cc_start: 0.8369 (mt) cc_final: 0.8166 (mt) REVERT: C 69 TYR cc_start: 0.8629 (m-80) cc_final: 0.8273 (m-10) REVERT: C 95 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8060 (tpm170) REVERT: C 111 ASN cc_start: 0.8566 (m110) cc_final: 0.8157 (m110) REVERT: C 119 MET cc_start: 0.8598 (ttm) cc_final: 0.8128 (tpp) REVERT: C 128 ASN cc_start: 0.9497 (t0) cc_final: 0.9193 (m-40) REVERT: C 140 LEU cc_start: 0.7391 (mm) cc_final: 0.7005 (mm) REVERT: C 149 THR cc_start: 0.8355 (p) cc_final: 0.8076 (m) REVERT: C 184 ASP cc_start: 0.7899 (m-30) cc_final: 0.7562 (m-30) REVERT: C 299 MET cc_start: 0.7648 (mmm) cc_final: 0.7231 (mmt) REVERT: C 329 ILE cc_start: 0.7649 (pt) cc_final: 0.7427 (pt) REVERT: D 1211 MET cc_start: 0.8323 (mpp) cc_final: 0.7993 (mpp) REVERT: D 1251 MET cc_start: 0.8910 (tpt) cc_final: 0.8212 (mmp) REVERT: D 1316 LEU cc_start: 0.9325 (tp) cc_final: 0.9075 (pp) REVERT: D 1343 ASN cc_start: 0.6715 (m-40) cc_final: 0.6379 (m110) REVERT: D 1349 ASN cc_start: 0.7006 (t0) cc_final: 0.6620 (t0) REVERT: D 1389 ASN cc_start: 0.8816 (m-40) cc_final: 0.8475 (t0) REVERT: D 1397 TYR cc_start: 0.7318 (m-80) cc_final: 0.6950 (m-80) REVERT: D 1408 ARG cc_start: 0.5229 (mmt180) cc_final: 0.4282 (mmm-85) REVERT: D 1428 CYS cc_start: 0.7157 (m) cc_final: 0.6866 (m) REVERT: D 1517 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6656 (tp30) REVERT: D 1520 ARG cc_start: 0.8536 (mtt90) cc_final: 0.7737 (mtm-85) REVERT: D 1565 THR cc_start: 0.4796 (p) cc_final: 0.4306 (p) REVERT: D 1626 ASP cc_start: 0.8538 (p0) cc_final: 0.8275 (p0) REVERT: D 1675 LYS cc_start: 0.8713 (tttt) cc_final: 0.8025 (ptpt) REVERT: D 1728 SER cc_start: 0.9295 (t) cc_final: 0.9094 (p) REVERT: D 1823 GLN cc_start: 0.9154 (tp40) cc_final: 0.8814 (tp-100) REVERT: D 1870 LEU cc_start: 0.8986 (tp) cc_final: 0.8519 (tp) REVERT: D 1903 GLN cc_start: 0.9877 (OUTLIER) cc_final: 0.9597 (pm20) REVERT: D 1906 PHE cc_start: 0.9786 (m-80) cc_final: 0.9455 (m-80) REVERT: E 107 PHE cc_start: 0.9199 (m-10) cc_final: 0.8803 (m-10) REVERT: E 143 TYR cc_start: 0.8408 (m-10) cc_final: 0.8069 (m-10) outliers start: 2 outliers final: 0 residues processed: 382 average time/residue: 0.2725 time to fit residues: 155.0232 Evaluate side-chains 291 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 59 GLN B 59 GLN B 101 HIS B 115 ASN B 121 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 371 HIS D1262 GLN ** D1409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1703 ASN E 30 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 16038 Z= 0.374 Angle : 0.730 10.037 21720 Z= 0.367 Chirality : 0.047 0.208 2405 Planarity : 0.005 0.062 2800 Dihedral : 7.034 90.119 2194 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.03 % 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: -0.39 (0.20), residues: 1943 helix: 0.28 (0.17), residues: 937 sheet: -0.73 (0.30), residues: 289 loop : -0.58 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.009 0.002 HIS B 275 PHE 0.030 0.002 PHE D1699 TYR 0.029 0.002 TYR C 294 ARG 0.018 0.001 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8459 (t70) cc_final: 0.7404 (p0) REVERT: A 49 GLN cc_start: 0.7393 (pt0) cc_final: 0.6776 (mt0) REVERT: A 107 GLU cc_start: 0.6885 (tt0) cc_final: 0.6647 (tt0) REVERT: A 111 ASN cc_start: 0.8247 (m110) cc_final: 0.7840 (m110) REVERT: A 128 ASN cc_start: 0.9020 (t0) cc_final: 0.8777 (t0) REVERT: A 154 ASP cc_start: 0.8132 (m-30) cc_final: 0.7727 (m-30) REVERT: A 179 ASP cc_start: 0.8770 (m-30) cc_final: 0.8425 (p0) REVERT: A 195 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8627 (pt0) REVERT: A 253 GLU cc_start: 0.7818 (mp0) cc_final: 0.6844 (mp0) REVERT: A 269 MET cc_start: 0.7366 (mmm) cc_final: 0.6830 (mtp) REVERT: A 296 ASN cc_start: 0.7441 (m-40) cc_final: 0.7170 (m-40) REVERT: A 355 MET cc_start: 0.8200 (mtt) cc_final: 0.7851 (tpp) REVERT: A 364 GLU cc_start: 0.8710 (pt0) cc_final: 0.8386 (pt0) REVERT: B 78 ASN cc_start: 0.8089 (t0) cc_final: 0.7555 (t0) REVERT: B 80 ASP cc_start: 0.8913 (m-30) cc_final: 0.8711 (p0) REVERT: B 92 ASN cc_start: 0.8477 (t0) cc_final: 0.8160 (t0) REVERT: B 95 ARG cc_start: 0.7665 (mtt180) cc_final: 0.6310 (tpm170) REVERT: B 111 ASN cc_start: 0.8322 (m-40) cc_final: 0.8022 (m110) REVERT: B 134 VAL cc_start: 0.8184 (t) cc_final: 0.7672 (p) REVERT: B 176 MET cc_start: 0.6051 (mtt) cc_final: 0.5799 (mtt) REVERT: B 184 ASP cc_start: 0.8485 (t0) cc_final: 0.8239 (m-30) REVERT: B 191 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8257 (mmtt) REVERT: B 196 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7427 (mtt180) REVERT: B 214 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8045 (tm-30) REVERT: B 242 LEU cc_start: 0.8231 (mm) cc_final: 0.7977 (mm) REVERT: B 246 GLN cc_start: 0.8350 (tt0) cc_final: 0.7918 (tm-30) REVERT: B 314 GLN cc_start: 0.6428 (tm-30) cc_final: 0.6102 (tm-30) REVERT: C 11 ASP cc_start: 0.8127 (t70) cc_final: 0.7183 (m-30) REVERT: C 91 TYR cc_start: 0.7677 (m-80) cc_final: 0.6886 (t80) REVERT: C 95 ARG cc_start: 0.8782 (mtt180) cc_final: 0.7923 (tpm170) REVERT: C 111 ASN cc_start: 0.8502 (m110) cc_final: 0.7938 (m110) REVERT: C 119 MET cc_start: 0.8543 (ttm) cc_final: 0.8164 (tpp) REVERT: C 149 THR cc_start: 0.8494 (p) cc_final: 0.8172 (m) REVERT: C 171 LEU cc_start: 0.8190 (mm) cc_final: 0.7977 (mm) REVERT: C 299 MET cc_start: 0.8286 (mmm) cc_final: 0.7859 (mmm) REVERT: D 1251 MET cc_start: 0.8810 (tpt) cc_final: 0.8038 (mmp) REVERT: D 1316 LEU cc_start: 0.9352 (tp) cc_final: 0.9084 (pp) REVERT: D 1349 ASN cc_start: 0.7197 (t0) cc_final: 0.6766 (t0) REVERT: D 1389 ASN cc_start: 0.8867 (m-40) cc_final: 0.8541 (t0) REVERT: D 1397 TYR cc_start: 0.7438 (m-80) cc_final: 0.6979 (m-80) REVERT: D 1403 LEU cc_start: 0.7031 (tp) cc_final: 0.6449 (tp) REVERT: D 1408 ARG cc_start: 0.5189 (mmt180) cc_final: 0.4768 (mmt180) REVERT: D 1428 CYS cc_start: 0.7380 (m) cc_final: 0.6967 (m) REVERT: D 1517 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6865 (tp30) REVERT: D 1565 THR cc_start: 0.4878 (p) cc_final: 0.4464 (p) REVERT: D 1626 ASP cc_start: 0.8687 (p0) cc_final: 0.8415 (p0) REVERT: D 1675 LYS cc_start: 0.8712 (tttt) cc_final: 0.7999 (ptpt) REVERT: D 1752 HIS cc_start: 0.7346 (m-70) cc_final: 0.6921 (m-70) REVERT: D 1870 LEU cc_start: 0.9006 (tp) cc_final: 0.8522 (tp) REVERT: D 1900 PHE cc_start: 0.9700 (t80) cc_final: 0.9266 (m-80) REVERT: D 1906 PHE cc_start: 0.9786 (m-80) cc_final: 0.9459 (m-80) REVERT: E 104 ARG cc_start: 0.9301 (mmm160) cc_final: 0.9003 (mmm160) REVERT: E 107 PHE cc_start: 0.9260 (m-10) cc_final: 0.8835 (m-10) outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.2827 time to fit residues: 144.8682 Evaluate side-chains 263 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.3980 chunk 169 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 12 ASN B 121 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16038 Z= 0.174 Angle : 0.630 10.565 21720 Z= 0.308 Chirality : 0.044 0.240 2405 Planarity : 0.004 0.060 2800 Dihedral : 6.770 87.307 2194 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.12 % Allowed : 1.72 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.20), residues: 1943 helix: 0.54 (0.18), residues: 930 sheet: -0.47 (0.31), residues: 286 loop : -0.46 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 340 HIS 0.009 0.001 HIS C 88 PHE 0.018 0.001 PHE E 117 TYR 0.034 0.001 TYR E 122 ARG 0.007 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 373 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8236 (t70) cc_final: 0.7250 (p0) REVERT: A 49 GLN cc_start: 0.7122 (pt0) cc_final: 0.6545 (mt0) REVERT: A 78 ASN cc_start: 0.7479 (t0) cc_final: 0.6785 (t0) REVERT: A 107 GLU cc_start: 0.6745 (tt0) cc_final: 0.5879 (tt0) REVERT: A 111 ASN cc_start: 0.8398 (m110) cc_final: 0.7902 (m110) REVERT: A 128 ASN cc_start: 0.9026 (t0) cc_final: 0.8769 (t0) REVERT: A 132 MET cc_start: 0.8203 (ppp) cc_final: 0.7742 (ppp) REVERT: A 137 GLN cc_start: 0.8307 (mt0) cc_final: 0.7781 (mp10) REVERT: A 154 ASP cc_start: 0.8311 (m-30) cc_final: 0.7794 (m-30) REVERT: A 179 ASP cc_start: 0.8736 (m-30) cc_final: 0.8324 (p0) REVERT: A 180 LEU cc_start: 0.8098 (tt) cc_final: 0.7804 (tt) REVERT: A 195 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8625 (pt0) REVERT: A 253 GLU cc_start: 0.7731 (mp0) cc_final: 0.6536 (mp0) REVERT: A 269 MET cc_start: 0.7506 (mmm) cc_final: 0.7273 (mtp) REVERT: A 270 GLU cc_start: 0.4688 (mm-30) cc_final: 0.4383 (mm-30) REVERT: A 291 LYS cc_start: 0.9089 (tptp) cc_final: 0.8642 (mmtt) REVERT: A 292 ASP cc_start: 0.8338 (m-30) cc_final: 0.7995 (m-30) REVERT: A 296 ASN cc_start: 0.7388 (m-40) cc_final: 0.7141 (m-40) REVERT: A 355 MET cc_start: 0.8153 (mtt) cc_final: 0.7781 (tpp) REVERT: A 373 LYS cc_start: 0.9331 (mmpt) cc_final: 0.8970 (mttt) REVERT: B 78 ASN cc_start: 0.7943 (t0) cc_final: 0.7261 (t0) REVERT: B 82 MET cc_start: 0.7289 (tpt) cc_final: 0.6911 (tpt) REVERT: B 92 ASN cc_start: 0.8524 (t0) cc_final: 0.8249 (t0) REVERT: B 95 ARG cc_start: 0.7671 (mtt180) cc_final: 0.6257 (tpm170) REVERT: B 111 ASN cc_start: 0.8264 (m-40) cc_final: 0.7824 (m110) REVERT: B 134 VAL cc_start: 0.8015 (t) cc_final: 0.7490 (p) REVERT: B 176 MET cc_start: 0.6052 (mtt) cc_final: 0.5778 (mtt) REVERT: B 184 ASP cc_start: 0.8449 (t0) cc_final: 0.8174 (m-30) REVERT: B 191 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8169 (mmtt) REVERT: B 214 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7860 (tm-30) REVERT: B 242 LEU cc_start: 0.8262 (mm) cc_final: 0.8049 (mm) REVERT: B 246 GLN cc_start: 0.8377 (tt0) cc_final: 0.7823 (tm-30) REVERT: B 350 SER cc_start: 0.7732 (t) cc_final: 0.7503 (t) REVERT: C 11 ASP cc_start: 0.8102 (t70) cc_final: 0.7092 (m-30) REVERT: C 95 ARG cc_start: 0.8750 (mtt180) cc_final: 0.7979 (tpm170) REVERT: C 111 ASN cc_start: 0.8461 (m110) cc_final: 0.8029 (m110) REVERT: C 119 MET cc_start: 0.8524 (ttm) cc_final: 0.8110 (tpp) REVERT: C 140 LEU cc_start: 0.7228 (mm) cc_final: 0.6884 (mm) REVERT: C 299 MET cc_start: 0.8338 (mmm) cc_final: 0.7896 (mmt) REVERT: C 329 ILE cc_start: 0.7629 (pt) cc_final: 0.7424 (pt) REVERT: D 1251 MET cc_start: 0.8843 (tpt) cc_final: 0.8170 (mmp) REVERT: D 1316 LEU cc_start: 0.9347 (tp) cc_final: 0.9045 (pp) REVERT: D 1349 ASN cc_start: 0.7121 (t0) cc_final: 0.6657 (t0) REVERT: D 1389 ASN cc_start: 0.8849 (m-40) cc_final: 0.8533 (t0) REVERT: D 1397 TYR cc_start: 0.7389 (m-80) cc_final: 0.7035 (m-80) REVERT: D 1408 ARG cc_start: 0.5140 (mmt180) cc_final: 0.4225 (mmm-85) REVERT: D 1428 CYS cc_start: 0.7397 (m) cc_final: 0.7118 (m) REVERT: D 1517 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6970 (tp30) REVERT: D 1626 ASP cc_start: 0.8660 (p0) cc_final: 0.8399 (p0) REVERT: D 1675 LYS cc_start: 0.8718 (tttt) cc_final: 0.7926 (ptpt) REVERT: D 1752 HIS cc_start: 0.7327 (m-70) cc_final: 0.6977 (m-70) REVERT: D 1823 GLN cc_start: 0.9098 (tp40) cc_final: 0.8679 (tp-100) REVERT: D 1870 LEU cc_start: 0.9022 (tp) cc_final: 0.8531 (tp) REVERT: D 1906 PHE cc_start: 0.9797 (m-80) cc_final: 0.9477 (m-80) REVERT: E 104 ARG cc_start: 0.9306 (mmm160) cc_final: 0.8988 (mmm160) REVERT: E 107 PHE cc_start: 0.9195 (m-10) cc_final: 0.8781 (m-80) outliers start: 2 outliers final: 0 residues processed: 374 average time/residue: 0.2649 time to fit residues: 149.8351 Evaluate side-chains 284 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 40.0000 chunk 21 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 137 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 371 HIS ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16038 Z= 0.194 Angle : 0.621 7.684 21720 Z= 0.303 Chirality : 0.044 0.252 2405 Planarity : 0.004 0.054 2800 Dihedral : 6.574 86.893 2194 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.70 % 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: -0.04 (0.20), residues: 1943 helix: 0.57 (0.18), residues: 933 sheet: -0.41 (0.31), residues: 286 loop : -0.48 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.009 0.001 HIS C 88 PHE 0.024 0.001 PHE D1548 TYR 0.031 0.001 TYR E 143 ARG 0.005 0.000 ARG E 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 349 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8214 (t70) cc_final: 0.7278 (p0) REVERT: A 49 GLN cc_start: 0.7110 (pt0) cc_final: 0.6534 (mt0) REVERT: A 78 ASN cc_start: 0.7471 (t0) cc_final: 0.6751 (t0) REVERT: A 107 GLU cc_start: 0.6840 (tt0) cc_final: 0.6008 (tt0) REVERT: A 111 ASN cc_start: 0.8400 (m110) cc_final: 0.7960 (m110) REVERT: A 128 ASN cc_start: 0.9047 (t0) cc_final: 0.8800 (t0) REVERT: A 132 MET cc_start: 0.8441 (ppp) cc_final: 0.8006 (ppp) REVERT: A 137 GLN cc_start: 0.8348 (mt0) cc_final: 0.7783 (mp10) REVERT: A 154 ASP cc_start: 0.8397 (m-30) cc_final: 0.7905 (m-30) REVERT: A 179 ASP cc_start: 0.8724 (m-30) cc_final: 0.8319 (p0) REVERT: A 180 LEU cc_start: 0.8062 (tt) cc_final: 0.7809 (tt) REVERT: A 195 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8675 (pt0) REVERT: A 253 GLU cc_start: 0.7720 (mp0) cc_final: 0.6508 (mp0) REVERT: A 270 GLU cc_start: 0.4712 (mm-30) cc_final: 0.4416 (mm-30) REVERT: A 291 LYS cc_start: 0.9052 (tptp) cc_final: 0.8596 (mmtt) REVERT: A 292 ASP cc_start: 0.8414 (m-30) cc_final: 0.8020 (m-30) REVERT: A 296 ASN cc_start: 0.7463 (m-40) cc_final: 0.7153 (m-40) REVERT: A 355 MET cc_start: 0.8209 (mtt) cc_final: 0.7928 (tpp) REVERT: A 373 LYS cc_start: 0.9313 (mmpt) cc_final: 0.8969 (mttt) REVERT: B 78 ASN cc_start: 0.7656 (t0) cc_final: 0.7428 (t0) REVERT: B 82 MET cc_start: 0.7159 (tpt) cc_final: 0.6959 (tpt) REVERT: B 92 ASN cc_start: 0.8527 (t0) cc_final: 0.8248 (t0) REVERT: B 95 ARG cc_start: 0.7657 (mtt180) cc_final: 0.6227 (tpm170) REVERT: B 111 ASN cc_start: 0.8223 (m-40) cc_final: 0.7860 (m110) REVERT: B 134 VAL cc_start: 0.7938 (t) cc_final: 0.7429 (p) REVERT: B 176 MET cc_start: 0.6075 (mtt) cc_final: 0.5807 (mtt) REVERT: B 184 ASP cc_start: 0.8446 (t0) cc_final: 0.8161 (m-30) REVERT: B 191 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8148 (mmtt) REVERT: B 214 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7850 (tm-30) REVERT: B 246 GLN cc_start: 0.8388 (tt0) cc_final: 0.7866 (tm-30) REVERT: B 350 SER cc_start: 0.7707 (t) cc_final: 0.7479 (t) REVERT: C 11 ASP cc_start: 0.8083 (t70) cc_final: 0.7044 (m-30) REVERT: C 95 ARG cc_start: 0.8736 (mtt180) cc_final: 0.7984 (tpm170) REVERT: C 111 ASN cc_start: 0.8442 (m110) cc_final: 0.7995 (m110) REVERT: C 119 MET cc_start: 0.8517 (ttm) cc_final: 0.8131 (tpp) REVERT: C 140 LEU cc_start: 0.7333 (mm) cc_final: 0.7005 (mm) REVERT: C 299 MET cc_start: 0.8216 (mmm) cc_final: 0.7773 (mmt) REVERT: D 1251 MET cc_start: 0.8811 (tpt) cc_final: 0.8104 (mmp) REVERT: D 1316 LEU cc_start: 0.9342 (tp) cc_final: 0.9023 (pp) REVERT: D 1349 ASN cc_start: 0.7145 (t0) cc_final: 0.6734 (t0) REVERT: D 1389 ASN cc_start: 0.8900 (m-40) cc_final: 0.8576 (t0) REVERT: D 1408 ARG cc_start: 0.5114 (mmt180) cc_final: 0.4217 (mmm-85) REVERT: D 1517 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6950 (tp30) REVERT: D 1626 ASP cc_start: 0.8639 (p0) cc_final: 0.8419 (p0) REVERT: D 1675 LYS cc_start: 0.8727 (tttt) cc_final: 0.7909 (ptpt) REVERT: D 1752 HIS cc_start: 0.7311 (m-70) cc_final: 0.6913 (m-70) REVERT: D 1823 GLN cc_start: 0.9092 (tp40) cc_final: 0.8666 (tp-100) REVERT: D 1870 LEU cc_start: 0.8993 (tp) cc_final: 0.8472 (tp) REVERT: D 1900 PHE cc_start: 0.9714 (t80) cc_final: 0.9254 (m-80) REVERT: D 1906 PHE cc_start: 0.9800 (m-80) cc_final: 0.9498 (m-80) REVERT: E 40 MET cc_start: 0.5227 (tpt) cc_final: 0.5027 (tpt) REVERT: E 104 ARG cc_start: 0.9302 (mmm160) cc_final: 0.8970 (mmm160) REVERT: E 107 PHE cc_start: 0.9184 (m-10) cc_final: 0.8759 (m-80) outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.2803 time to fit residues: 146.9473 Evaluate side-chains 285 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 119 optimal weight: 0.0570 chunk 128 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 147 optimal weight: 0.0170 chunk 170 optimal weight: 0.6980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 371 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16038 Z= 0.159 Angle : 0.617 7.816 21720 Z= 0.299 Chirality : 0.043 0.160 2405 Planarity : 0.004 0.051 2800 Dihedral : 6.381 83.135 2194 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.12 % Allowed : 0.95 % Favored : 98.93 % 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: 0.03 (0.20), residues: 1943 helix: 0.60 (0.18), residues: 927 sheet: -0.33 (0.31), residues: 286 loop : -0.41 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D1550 HIS 0.008 0.001 HIS C 88 PHE 0.021 0.001 PHE E 34 TYR 0.028 0.001 TYR C 294 ARG 0.008 0.000 ARG E 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 355 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8170 (t70) cc_final: 0.7233 (p0) REVERT: A 78 ASN cc_start: 0.7464 (t0) cc_final: 0.6729 (t0) REVERT: A 107 GLU cc_start: 0.6847 (tt0) cc_final: 0.5799 (tt0) REVERT: A 111 ASN cc_start: 0.8473 (m110) cc_final: 0.7943 (m110) REVERT: A 128 ASN cc_start: 0.9038 (t0) cc_final: 0.8788 (t0) REVERT: A 132 MET cc_start: 0.8460 (ppp) cc_final: 0.8045 (ppp) REVERT: A 137 GLN cc_start: 0.8401 (mt0) cc_final: 0.7852 (mp10) REVERT: A 154 ASP cc_start: 0.8420 (m-30) cc_final: 0.8067 (m-30) REVERT: A 179 ASP cc_start: 0.8849 (m-30) cc_final: 0.8364 (p0) REVERT: A 180 LEU cc_start: 0.8084 (tt) cc_final: 0.7785 (tt) REVERT: A 195 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8730 (pt0) REVERT: A 250 ILE cc_start: 0.7476 (mt) cc_final: 0.6971 (mt) REVERT: A 253 GLU cc_start: 0.7616 (mp0) cc_final: 0.6992 (pm20) REVERT: A 291 LYS cc_start: 0.9088 (tptp) cc_final: 0.8641 (mmtt) REVERT: A 292 ASP cc_start: 0.8393 (m-30) cc_final: 0.8017 (m-30) REVERT: A 296 ASN cc_start: 0.7483 (m-40) cc_final: 0.7175 (m-40) REVERT: A 326 LYS cc_start: 0.8937 (tppt) cc_final: 0.8707 (tmtt) REVERT: A 355 MET cc_start: 0.8148 (mtt) cc_final: 0.7935 (mmm) REVERT: A 373 LYS cc_start: 0.9295 (mmpt) cc_final: 0.8967 (mttt) REVERT: B 50 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7703 (mttm) REVERT: B 78 ASN cc_start: 0.7675 (t0) cc_final: 0.7427 (t0) REVERT: B 92 ASN cc_start: 0.8529 (t0) cc_final: 0.8274 (t0) REVERT: B 95 ARG cc_start: 0.7694 (mtt180) cc_final: 0.6243 (tpm170) REVERT: B 111 ASN cc_start: 0.8244 (m-40) cc_final: 0.7841 (m110) REVERT: B 134 VAL cc_start: 0.7772 (t) cc_final: 0.7206 (p) REVERT: B 176 MET cc_start: 0.6065 (mtt) cc_final: 0.5801 (mtt) REVERT: B 184 ASP cc_start: 0.8419 (t0) cc_final: 0.8142 (m-30) REVERT: B 191 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8096 (mmtt) REVERT: B 214 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7732 (tm-30) REVERT: B 246 GLN cc_start: 0.8291 (tt0) cc_final: 0.7843 (tm-30) REVERT: B 314 GLN cc_start: 0.6237 (tm-30) cc_final: 0.5946 (tm-30) REVERT: B 350 SER cc_start: 0.7744 (t) cc_final: 0.7513 (t) REVERT: C 11 ASP cc_start: 0.7952 (t70) cc_final: 0.6949 (m-30) REVERT: C 95 ARG cc_start: 0.8679 (mtt180) cc_final: 0.7937 (tpm170) REVERT: C 111 ASN cc_start: 0.8479 (m110) cc_final: 0.7994 (m110) REVERT: C 119 MET cc_start: 0.8518 (ttm) cc_final: 0.8125 (tpp) REVERT: C 140 LEU cc_start: 0.7212 (mm) cc_final: 0.6851 (mm) REVERT: C 280 ASN cc_start: 0.7937 (m-40) cc_final: 0.7598 (t0) REVERT: C 299 MET cc_start: 0.8124 (mmm) cc_final: 0.7638 (mmt) REVERT: D 1251 MET cc_start: 0.8802 (tpt) cc_final: 0.8074 (mmp) REVERT: D 1316 LEU cc_start: 0.9331 (tp) cc_final: 0.8995 (pp) REVERT: D 1349 ASN cc_start: 0.7147 (t0) cc_final: 0.6740 (t0) REVERT: D 1389 ASN cc_start: 0.8917 (m-40) cc_final: 0.8594 (t0) REVERT: D 1408 ARG cc_start: 0.5180 (mmt180) cc_final: 0.4289 (mmm-85) REVERT: D 1517 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6929 (tp30) REVERT: D 1626 ASP cc_start: 0.8679 (p0) cc_final: 0.8468 (p0) REVERT: D 1651 PHE cc_start: 0.6313 (t80) cc_final: 0.6044 (t80) REVERT: D 1675 LYS cc_start: 0.8805 (tttt) cc_final: 0.7950 (ptpt) REVERT: D 1752 HIS cc_start: 0.7212 (m-70) cc_final: 0.6848 (m-70) REVERT: D 1823 GLN cc_start: 0.9085 (tp40) cc_final: 0.8640 (tp-100) REVERT: D 1870 LEU cc_start: 0.9010 (tp) cc_final: 0.8493 (tp) REVERT: D 1900 PHE cc_start: 0.9713 (t80) cc_final: 0.9278 (m-80) REVERT: D 1906 PHE cc_start: 0.9795 (m-80) cc_final: 0.9481 (m-80) REVERT: E 103 ILE cc_start: 0.9030 (mt) cc_final: 0.8369 (mt) REVERT: E 104 ARG cc_start: 0.9327 (mmm160) cc_final: 0.9019 (mmm160) REVERT: E 143 TYR cc_start: 0.8566 (m-10) cc_final: 0.8362 (m-80) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.2655 time to fit residues: 141.6263 Evaluate side-chains 284 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 158 optimal weight: 0.1980 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 371 HIS ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16038 Z= 0.185 Angle : 0.633 14.076 21720 Z= 0.305 Chirality : 0.044 0.190 2405 Planarity : 0.004 0.049 2800 Dihedral : 6.290 81.377 2194 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.01 (0.20), residues: 1943 helix: 0.59 (0.18), residues: 927 sheet: -0.36 (0.32), residues: 280 loop : -0.45 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 340 HIS 0.007 0.001 HIS C 88 PHE 0.040 0.001 PHE E 107 TYR 0.026 0.001 TYR C 294 ARG 0.019 0.000 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8215 (t70) cc_final: 0.7158 (p0) REVERT: A 49 GLN cc_start: 0.6990 (pt0) cc_final: 0.6560 (mt0) REVERT: A 78 ASN cc_start: 0.7466 (t0) cc_final: 0.6738 (t0) REVERT: A 111 ASN cc_start: 0.8463 (m110) cc_final: 0.7938 (m110) REVERT: A 123 MET cc_start: 0.8876 (tpp) cc_final: 0.8566 (tpp) REVERT: A 128 ASN cc_start: 0.9039 (t0) cc_final: 0.8792 (t0) REVERT: A 132 MET cc_start: 0.8482 (ppp) cc_final: 0.8011 (ppp) REVERT: A 137 GLN cc_start: 0.8513 (mt0) cc_final: 0.8217 (mp10) REVERT: A 154 ASP cc_start: 0.8398 (m-30) cc_final: 0.8051 (m-30) REVERT: A 179 ASP cc_start: 0.8794 (m-30) cc_final: 0.8557 (p0) REVERT: A 195 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8738 (pt0) REVERT: A 250 ILE cc_start: 0.7448 (mt) cc_final: 0.6953 (mt) REVERT: A 253 GLU cc_start: 0.7619 (mp0) cc_final: 0.7028 (pm20) REVERT: A 296 ASN cc_start: 0.7508 (m-40) cc_final: 0.7158 (m-40) REVERT: A 299 MET cc_start: 0.8217 (mmp) cc_final: 0.7932 (mmp) REVERT: A 326 LYS cc_start: 0.8947 (tppt) cc_final: 0.8735 (tmtt) REVERT: A 373 LYS cc_start: 0.9301 (mmpt) cc_final: 0.8979 (mttt) REVERT: B 50 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7839 (mttm) REVERT: B 78 ASN cc_start: 0.7675 (t0) cc_final: 0.7448 (t0) REVERT: B 92 ASN cc_start: 0.8533 (t0) cc_final: 0.8272 (t0) REVERT: B 95 ARG cc_start: 0.7697 (mtt180) cc_final: 0.6226 (tpm170) REVERT: B 111 ASN cc_start: 0.8216 (m-40) cc_final: 0.7972 (m110) REVERT: B 134 VAL cc_start: 0.7714 (t) cc_final: 0.7178 (p) REVERT: B 167 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7595 (mp0) REVERT: B 176 MET cc_start: 0.6076 (mtt) cc_final: 0.5819 (mtt) REVERT: B 184 ASP cc_start: 0.8410 (t0) cc_final: 0.8133 (m-30) REVERT: B 191 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8153 (mmtt) REVERT: B 214 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7756 (tm-30) REVERT: B 246 GLN cc_start: 0.8292 (tt0) cc_final: 0.7855 (tm-30) REVERT: B 314 GLN cc_start: 0.6280 (tm-30) cc_final: 0.5977 (tm-30) REVERT: B 350 SER cc_start: 0.7663 (t) cc_final: 0.7438 (t) REVERT: C 11 ASP cc_start: 0.8113 (t70) cc_final: 0.7069 (m-30) REVERT: C 95 ARG cc_start: 0.8678 (mtt180) cc_final: 0.7954 (tpm170) REVERT: C 101 HIS cc_start: 0.7953 (m170) cc_final: 0.7748 (m170) REVERT: C 111 ASN cc_start: 0.8471 (m110) cc_final: 0.8025 (m110) REVERT: C 119 MET cc_start: 0.8551 (ttm) cc_final: 0.8238 (tpp) REVERT: C 280 ASN cc_start: 0.7920 (m-40) cc_final: 0.7566 (t0) REVERT: C 299 MET cc_start: 0.7896 (mmm) cc_final: 0.7395 (mmt) REVERT: D 1246 VAL cc_start: 0.9616 (m) cc_final: 0.9406 (p) REVERT: D 1251 MET cc_start: 0.8801 (tpt) cc_final: 0.8063 (mmp) REVERT: D 1316 LEU cc_start: 0.9341 (tp) cc_final: 0.9008 (pp) REVERT: D 1330 LYS cc_start: 0.8904 (pttm) cc_final: 0.8318 (ptmm) REVERT: D 1349 ASN cc_start: 0.7133 (t0) cc_final: 0.6704 (t0) REVERT: D 1389 ASN cc_start: 0.8919 (m-40) cc_final: 0.8592 (t0) REVERT: D 1408 ARG cc_start: 0.5135 (mmt180) cc_final: 0.4209 (mmm-85) REVERT: D 1517 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6875 (tp30) REVERT: D 1550 TRP cc_start: 0.8619 (t60) cc_final: 0.8373 (t-100) REVERT: D 1626 ASP cc_start: 0.8715 (p0) cc_final: 0.8510 (p0) REVERT: D 1651 PHE cc_start: 0.6280 (t80) cc_final: 0.5945 (t80) REVERT: D 1675 LYS cc_start: 0.8706 (tttt) cc_final: 0.7881 (ptpt) REVERT: D 1752 HIS cc_start: 0.7121 (m-70) cc_final: 0.6773 (m-70) REVERT: D 1823 GLN cc_start: 0.9006 (tp40) cc_final: 0.8559 (tp-100) REVERT: D 1870 LEU cc_start: 0.9006 (tp) cc_final: 0.8478 (tp) REVERT: D 1906 PHE cc_start: 0.9803 (m-80) cc_final: 0.9482 (m-80) REVERT: E 103 ILE cc_start: 0.9063 (mt) cc_final: 0.8802 (mt) REVERT: E 104 ARG cc_start: 0.9371 (mmm160) cc_final: 0.9023 (mmm160) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2711 time to fit residues: 143.9151 Evaluate side-chains 287 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.0270 chunk 194 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 154 optimal weight: 0.0970 chunk 16 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 12 ASN C 371 HIS ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16038 Z= 0.201 Angle : 0.635 8.584 21720 Z= 0.306 Chirality : 0.044 0.166 2405 Planarity : 0.004 0.047 2800 Dihedral : 6.281 79.497 2194 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.76 % 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: 0.03 (0.20), residues: 1943 helix: 0.64 (0.18), residues: 927 sheet: -0.48 (0.31), residues: 287 loop : -0.38 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.007 0.001 HIS C 88 PHE 0.023 0.001 PHE B 223 TYR 0.025 0.001 TYR C 294 ARG 0.016 0.000 ARG E 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3886 Ramachandran restraints generated. 1943 Oldfield, 0 Emsley, 1943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.8297 (t70) cc_final: 0.7029 (p0) REVERT: A 49 GLN cc_start: 0.7032 (pt0) cc_final: 0.6430 (mt0) REVERT: A 78 ASN cc_start: 0.7482 (t0) cc_final: 0.6745 (t0) REVERT: A 107 GLU cc_start: 0.6768 (tt0) cc_final: 0.5370 (tt0) REVERT: A 111 ASN cc_start: 0.8496 (m110) cc_final: 0.7978 (m110) REVERT: A 128 ASN cc_start: 0.9062 (t0) cc_final: 0.8826 (t0) REVERT: A 132 MET cc_start: 0.8577 (ppp) cc_final: 0.8094 (ppp) REVERT: A 137 GLN cc_start: 0.8588 (mt0) cc_final: 0.8123 (mp10) REVERT: A 195 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8652 (pt0) REVERT: A 253 GLU cc_start: 0.7688 (mp0) cc_final: 0.6350 (mp0) REVERT: A 285 CYS cc_start: 0.7656 (p) cc_final: 0.7348 (p) REVERT: A 296 ASN cc_start: 0.7570 (m-40) cc_final: 0.7208 (m-40) REVERT: A 299 MET cc_start: 0.8114 (mmp) cc_final: 0.7883 (mmp) REVERT: A 326 LYS cc_start: 0.9017 (tppt) cc_final: 0.8763 (tmtt) REVERT: A 364 GLU cc_start: 0.8791 (pt0) cc_final: 0.8038 (pt0) REVERT: A 373 LYS cc_start: 0.9264 (mmpt) cc_final: 0.8888 (tptt) REVERT: B 50 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7797 (mttm) REVERT: B 78 ASN cc_start: 0.7724 (t0) cc_final: 0.7406 (t0) REVERT: B 82 MET cc_start: 0.7156 (tpt) cc_final: 0.6795 (tpt) REVERT: B 92 ASN cc_start: 0.8531 (t0) cc_final: 0.8253 (t0) REVERT: B 95 ARG cc_start: 0.7700 (mtt180) cc_final: 0.6188 (tpm170) REVERT: B 111 ASN cc_start: 0.8245 (m-40) cc_final: 0.7993 (m110) REVERT: B 134 VAL cc_start: 0.7658 (t) cc_final: 0.7174 (p) REVERT: B 184 ASP cc_start: 0.8400 (t0) cc_final: 0.8136 (m-30) REVERT: B 191 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8171 (mmtt) REVERT: B 205 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7892 (mp0) REVERT: B 214 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7790 (tm-30) REVERT: B 314 GLN cc_start: 0.6258 (tm-30) cc_final: 0.5949 (tm-30) REVERT: B 350 SER cc_start: 0.7676 (t) cc_final: 0.7451 (t) REVERT: C 11 ASP cc_start: 0.8076 (t70) cc_final: 0.7052 (m-30) REVERT: C 95 ARG cc_start: 0.8673 (mtt180) cc_final: 0.7927 (tpm170) REVERT: C 101 HIS cc_start: 0.8030 (m170) cc_final: 0.7737 (m170) REVERT: C 111 ASN cc_start: 0.8446 (m110) cc_final: 0.8001 (m110) REVERT: C 119 MET cc_start: 0.8520 (ttm) cc_final: 0.8182 (tpp) REVERT: C 269 MET cc_start: 0.8083 (mtt) cc_final: 0.7882 (mtm) REVERT: C 280 ASN cc_start: 0.7919 (m-40) cc_final: 0.7571 (t0) REVERT: C 299 MET cc_start: 0.7861 (mmm) cc_final: 0.7467 (mmm) REVERT: D 1246 VAL cc_start: 0.9635 (m) cc_final: 0.9407 (p) REVERT: D 1251 MET cc_start: 0.8759 (tpt) cc_final: 0.7975 (mmp) REVERT: D 1316 LEU cc_start: 0.9339 (tp) cc_final: 0.9008 (pp) REVERT: D 1330 LYS cc_start: 0.8867 (pttm) cc_final: 0.8261 (ptmm) REVERT: D 1349 ASN cc_start: 0.7221 (t0) cc_final: 0.6789 (t0) REVERT: D 1389 ASN cc_start: 0.8913 (m-40) cc_final: 0.8586 (t0) REVERT: D 1517 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6985 (tp30) REVERT: D 1550 TRP cc_start: 0.8630 (t60) cc_final: 0.8375 (t60) REVERT: D 1675 LYS cc_start: 0.8705 (tttt) cc_final: 0.7864 (ptpt) REVERT: D 1752 HIS cc_start: 0.7054 (m-70) cc_final: 0.6726 (m-70) REVERT: D 1823 GLN cc_start: 0.9035 (tp40) cc_final: 0.8562 (tp40) REVERT: D 1870 LEU cc_start: 0.9006 (tp) cc_final: 0.8463 (tp) REVERT: D 1900 PHE cc_start: 0.9715 (t80) cc_final: 0.9300 (m-80) REVERT: D 1906 PHE cc_start: 0.9807 (m-80) cc_final: 0.9491 (m-80) REVERT: E 104 ARG cc_start: 0.9403 (mmm160) cc_final: 0.9019 (mpt180) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2734 time to fit residues: 141.5593 Evaluate side-chains 271 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 173 HIS C 371 HIS ** D1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1595 ASN ** D1664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090333 restraints weight = 40120.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092430 restraints weight = 23485.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093849 restraints weight = 15840.837| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16038 Z= 0.212 Angle : 0.633 8.634 21720 Z= 0.307 Chirality : 0.044 0.156 2405 Planarity : 0.004 0.047 2800 Dihedral : 6.300 76.481 2194 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.53 % 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: 0.02 (0.20), residues: 1943 helix: 0.63 (0.18), residues: 925 sheet: -0.46 (0.31), residues: 291 loop : -0.42 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.007 0.001 HIS C 88 PHE 0.024 0.001 PHE B 223 TYR 0.025 0.001 TYR C 294 ARG 0.014 0.000 ARG E 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3979.92 seconds wall clock time: 73 minutes 17.71 seconds (4397.71 seconds total)