Starting phenix.real_space_refine on Fri Feb 16 04:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2024/7rb8_24399_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2024/7rb8_24399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2024/7rb8_24399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2024/7rb8_24399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2024/7rb8_24399_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb8_24399/02_2024/7rb8_24399_updated.pdb" } resolution = 3.63 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= 0.003 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 91 5.16 5 C 9000 2.51 5 N 2418 2.21 5 O 2705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "D TYR 1420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1537": "OD1" <-> "OD2" Residue "D TYR 1639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 364": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14226 Number of models: 1 Model: "" Number of chains: 8 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: "D" Number of atoms: 5363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5363 Classifications: {'peptide': 667} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 643} Chain breaks: 2 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: "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: "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} 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} Time building chain proxies: 7.58, per 1000 atoms: 0.53 Number of scatterers: 14226 At special positions: 0 Unit cell: (110.21, 151.41, 139.05, 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 91 16.00 P 8 15.00 Mg 4 11.99 O 2705 8.00 N 2418 7.00 C 9000 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: 5.60 Conformation dependent library (CDL) restraints added in 2.3 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 15 sheets defined 45.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 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: 3.555A 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 '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: 3.623A pdb=" N ILE D1278 " --> pdb=" O LEU D1275 " (cutoff:3.500A) removed outlier: 3.746A 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: 3.545A 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: 3.702A 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 1822 through 1828 Processing helix chain 'D' and resid 1847 through 1853 Processing helix chain 'D' and resid 1872 through 1885 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: 4.979A 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: 3.628A 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: 3.555A 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: 3.506A 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: 3.954A 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: 3.811A 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: 3.505A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.131A 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 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: 8.747A 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 'D' and resid 1237 through 1239 removed outlier: 7.989A pdb=" N VAL D1295 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 5.607A 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= F, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id= G, first strand: chain 'D' and resid 1682 through 1687 Processing sheet with id= H, 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: 6.423A 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= I, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= J, 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= K, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= L, 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= M, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= N, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.917A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 241 558 hydrogen bonds defined for protein. 1515 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: 5.24 Time building geometry restraints manager: 5.97 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: 2958 1.33 - 1.45: 3299 1.45 - 1.57: 8101 1.57 - 1.69: 12 1.69 - 1.82: 153 Bond restraints: 14523 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 8.35e+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 8.34e+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 8.32e+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 6.19e+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 4.90e+00 ... (remaining 14518 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.60: 474 106.60 - 114.00: 8260 114.00 - 121.41: 7470 121.41 - 128.81: 3398 128.81 - 136.22: 85 Bond angle restraints: 19687 Sorted by residual: angle pdb=" N ILE D1865 " pdb=" CA ILE D1865 " pdb=" C ILE D1865 " ideal model delta sigma weight residual 111.56 104.82 6.74 8.60e-01 1.35e+00 6.15e+01 angle pdb=" C GLY D1256 " pdb=" N PRO D1257 " pdb=" CA PRO D1257 " ideal model delta sigma weight residual 119.56 113.04 6.52 1.01e+00 9.80e-01 4.17e+01 angle pdb=" N ASN D1320 " pdb=" CA ASN D1320 " pdb=" C ASN D1320 " ideal model delta sigma weight residual 109.76 101.09 8.67 1.64e+00 3.72e-01 2.80e+01 angle pdb=" N ILE D1242 " pdb=" CA ILE D1242 " pdb=" C ILE D1242 " ideal model delta sigma weight residual 109.55 116.54 -6.99 1.38e+00 5.25e-01 2.57e+01 angle pdb=" C ILE D1239 " pdb=" CA ILE D1239 " pdb=" CB ILE D1239 " ideal model delta sigma weight residual 113.22 108.32 4.90 1.12e+00 7.97e-01 1.92e+01 ... (remaining 19682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 8235 23.36 - 46.72: 462 46.72 - 70.07: 51 70.07 - 93.43: 12 93.43 - 116.79: 4 Dihedral angle restraints: 8764 sinusoidal: 3564 harmonic: 5200 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 -176.79 116.79 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 -176.79 116.79 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 -176.78 116.78 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 8761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1649 0.049 - 0.097: 416 0.097 - 0.146: 117 0.146 - 0.195: 7 0.195 - 0.244: 5 Chirality restraints: 2194 Sorted by residual: 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 0.24 2.00e-01 2.50e+01 1.48e+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 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LYS D1867 " pdb=" N LYS D1867 " pdb=" C LYS D1867 " pdb=" CB LYS D1867 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2191 not shown) Planarity restraints: 2528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D1251 " 0.016 2.00e-02 2.50e+03 3.23e-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 2.82e-02 7.95e+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 4.07e-02 2.65e+00 pdb=" N PRO A 243 " -0.070 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 2525 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 50 2.52 - 3.11: 10510 3.11 - 3.71: 21643 3.71 - 4.30: 29653 4.30 - 4.90: 50375 Nonbonded interactions: 112231 Sorted by model distance: nonbonded pdb=" O LEU D1837 " pdb=" CD1 LEU D1837 " model vdw 1.921 3.460 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 2.186 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" O LEU D1377 " pdb=" OH TYR D1574 " model vdw 2.256 2.440 ... (remaining 112226 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: 7.480 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: 27.110 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.190 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 14523 Z= 0.241 Angle : 0.676 9.614 19687 Z= 0.376 Chirality : 0.046 0.244 2194 Planarity : 0.004 0.041 2528 Dihedral : 14.222 116.791 5418 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % 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: -0.17 (0.21), residues: 1765 helix: 0.73 (0.19), residues: 823 sheet: -1.06 (0.30), residues: 288 loop : -0.59 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D1619 HIS 0.003 0.001 HIS D1666 PHE 0.013 0.001 PHE D1699 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) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: D 1286 MET cc_start: 0.7508 (ptp) cc_final: 0.7169 (ptm) REVERT: D 1881 MET cc_start: 0.8726 (tmm) cc_final: 0.8412 (ppp) REVERT: B 95 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7180 (mmt180) REVERT: C 95 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7376 (mmt180) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2661 time to fit residues: 71.5630 Evaluate side-chains 110 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 0.0060 chunk 103 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 14523 Z= 0.421 Angle : 0.676 9.003 19687 Z= 0.334 Chirality : 0.048 0.211 2194 Planarity : 0.004 0.043 2528 Dihedral : 7.301 105.067 1997 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.78 % Allowed : 7.13 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1765 helix: 0.62 (0.19), residues: 820 sheet: -1.03 (0.30), residues: 279 loop : -0.70 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D1550 HIS 0.006 0.001 HIS D1666 PHE 0.019 0.001 PHE D1699 TYR 0.018 0.002 TYR C 337 ARG 0.004 0.000 ARG D1491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: D 1881 MET cc_start: 0.8737 (tmm) cc_final: 0.8414 (ppp) REVERT: B 95 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7247 (mmt180) REVERT: B 288 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6706 (m-30) REVERT: B 370 VAL cc_start: 0.9381 (p) cc_final: 0.9154 (p) REVERT: C 95 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7405 (mmt180) REVERT: C 184 ASP cc_start: 0.7722 (t0) cc_final: 0.7508 (t0) outliers start: 12 outliers final: 5 residues processed: 122 average time/residue: 0.2501 time to fit residues: 47.3107 Evaluate side-chains 109 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 109 optimal weight: 0.0970 chunk 44 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 0.0980 chunk 143 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 14523 Z= 0.140 Angle : 0.550 7.346 19687 Z= 0.265 Chirality : 0.042 0.174 2194 Planarity : 0.004 0.037 2528 Dihedral : 6.679 94.754 1997 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.98 % Allowed : 8.89 % Favored : 90.12 % 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: 0.20 (0.21), residues: 1765 helix: 0.92 (0.19), residues: 811 sheet: -0.65 (0.31), residues: 274 loop : -0.34 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D1550 HIS 0.003 0.001 HIS C 101 PHE 0.011 0.001 PHE D1451 TYR 0.019 0.001 TYR D1255 ARG 0.003 0.000 ARG D1491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8396 (mmm) cc_final: 0.8146 (mtp) REVERT: D 1762 LEU cc_start: 0.9264 (tp) cc_final: 0.9029 (tt) REVERT: D 1881 MET cc_start: 0.8819 (tmm) cc_final: 0.8456 (ppp) REVERT: B 95 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7215 (mmt180) REVERT: B 294 TYR cc_start: 0.8480 (m-10) cc_final: 0.8238 (m-10) REVERT: B 370 VAL cc_start: 0.9328 (p) cc_final: 0.9077 (p) REVERT: C 95 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7380 (mmt180) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.2513 time to fit residues: 50.6870 Evaluate side-chains 115 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1409 GLN Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 0.0060 chunk 161 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14523 Z= 0.212 Angle : 0.556 7.003 19687 Z= 0.267 Chirality : 0.043 0.253 2194 Planarity : 0.004 0.037 2528 Dihedral : 6.468 90.248 1997 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.70 % Allowed : 10.33 % Favored : 87.97 % 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: 0.25 (0.21), residues: 1765 helix: 0.94 (0.19), residues: 813 sheet: -0.66 (0.29), residues: 291 loop : -0.24 (0.27), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D1550 HIS 0.003 0.001 HIS D1666 PHE 0.010 0.001 PHE D1451 TYR 0.016 0.001 TYR D1255 ARG 0.002 0.000 ARG D1491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 192 ILE cc_start: 0.9402 (tp) cc_final: 0.9109 (tp) REVERT: D 1881 MET cc_start: 0.8825 (tmm) cc_final: 0.8460 (ppp) REVERT: B 95 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7251 (mmt180) REVERT: C 95 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7409 (mmt180) REVERT: C 299 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8050 (mmm) outliers start: 26 outliers final: 10 residues processed: 128 average time/residue: 0.2347 time to fit residues: 47.5050 Evaluate side-chains 115 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1409 GLN Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 153 optimal weight: 0.3980 chunk 43 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14523 Z= 0.312 Angle : 0.609 7.847 19687 Z= 0.296 Chirality : 0.045 0.173 2194 Planarity : 0.004 0.039 2528 Dihedral : 6.544 90.134 1997 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.50 % Allowed : 10.86 % Favored : 87.64 % 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: 0.16 (0.21), residues: 1765 helix: 0.88 (0.19), residues: 815 sheet: -0.67 (0.30), residues: 279 loop : -0.34 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1550 HIS 0.004 0.001 HIS D1666 PHE 0.013 0.001 PHE D1699 TYR 0.015 0.001 TYR D1255 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: A 192 ILE cc_start: 0.9421 (tp) cc_final: 0.9104 (tp) REVERT: A 259 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: D 1699 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: D 1881 MET cc_start: 0.8833 (tmm) cc_final: 0.8458 (ppp) REVERT: B 95 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7268 (mmt180) REVERT: B 288 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6410 (m-30) REVERT: B 299 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: C 47 MET cc_start: 0.7752 (mtt) cc_final: 0.6777 (ptt) REVERT: C 95 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7486 (mmt180) REVERT: C 299 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8105 (mmm) outliers start: 23 outliers final: 10 residues processed: 127 average time/residue: 0.2346 time to fit residues: 47.4617 Evaluate side-chains 116 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1409 GLN Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1699 PHE Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.0040 chunk 89 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14523 Z= 0.161 Angle : 0.550 6.961 19687 Z= 0.264 Chirality : 0.042 0.138 2194 Planarity : 0.003 0.036 2528 Dihedral : 6.224 82.930 1997 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.31 % Allowed : 11.12 % Favored : 87.57 % 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: 0.35 (0.21), residues: 1765 helix: 1.00 (0.19), residues: 812 sheet: -0.55 (0.29), residues: 291 loop : -0.21 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.004 0.001 HIS C 88 PHE 0.010 0.001 PHE D1341 TYR 0.015 0.001 TYR D1255 ARG 0.002 0.000 ARG D1491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 192 ILE cc_start: 0.9412 (tp) cc_final: 0.9112 (tp) REVERT: A 305 MET cc_start: 0.8373 (mmm) cc_final: 0.8125 (mtp) REVERT: D 1699 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8030 (m-10) REVERT: D 1881 MET cc_start: 0.8810 (tmm) cc_final: 0.8446 (ppp) REVERT: B 95 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7214 (mmt180) REVERT: C 47 MET cc_start: 0.7690 (mtt) cc_final: 0.6774 (ptt) REVERT: C 95 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7465 (mmt180) REVERT: C 299 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8316 (mmm) outliers start: 20 outliers final: 10 residues processed: 122 average time/residue: 0.2398 time to fit residues: 46.3361 Evaluate side-chains 114 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1409 GLN Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1699 PHE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 170 optimal weight: 0.0470 chunk 106 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14523 Z= 0.162 Angle : 0.548 7.862 19687 Z= 0.260 Chirality : 0.042 0.136 2194 Planarity : 0.003 0.035 2528 Dihedral : 5.882 75.184 1997 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.24 % Allowed : 11.45 % Favored : 87.31 % 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: 0.46 (0.21), residues: 1765 helix: 1.07 (0.19), residues: 811 sheet: -0.47 (0.29), residues: 291 loop : -0.12 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 340 HIS 0.003 0.001 HIS C 88 PHE 0.011 0.001 PHE D1341 TYR 0.014 0.001 TYR D1255 ARG 0.001 0.000 ARG D1491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: A 192 ILE cc_start: 0.9404 (tp) cc_final: 0.9100 (tp) REVERT: A 305 MET cc_start: 0.8433 (mmm) cc_final: 0.8192 (mtp) REVERT: D 1699 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8089 (m-10) REVERT: D 1881 MET cc_start: 0.8833 (tmm) cc_final: 0.8479 (ppp) REVERT: B 95 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7243 (mmt180) REVERT: C 47 MET cc_start: 0.7687 (mtt) cc_final: 0.6756 (ptt) REVERT: C 95 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7480 (mmt180) REVERT: C 299 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8301 (mmm) outliers start: 19 outliers final: 8 residues processed: 125 average time/residue: 0.2356 time to fit residues: 47.1098 Evaluate side-chains 115 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1409 GLN Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1699 PHE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 0.0470 chunk 155 optimal weight: 0.5980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14523 Z= 0.163 Angle : 0.556 8.872 19687 Z= 0.262 Chirality : 0.042 0.156 2194 Planarity : 0.003 0.035 2528 Dihedral : 5.656 68.175 1997 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.05 % Allowed : 12.36 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.21), residues: 1765 helix: 1.08 (0.19), residues: 813 sheet: -0.44 (0.30), residues: 291 loop : -0.09 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.003 0.001 HIS C 88 PHE 0.009 0.001 PHE D1341 TYR 0.013 0.001 TYR D1255 ARG 0.004 0.000 ARG D1408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: A 192 ILE cc_start: 0.9399 (tp) cc_final: 0.9094 (tp) REVERT: A 305 MET cc_start: 0.8451 (mmm) cc_final: 0.8187 (mtp) REVERT: D 1699 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8128 (m-10) REVERT: D 1881 MET cc_start: 0.8864 (tmm) cc_final: 0.8485 (ppp) REVERT: B 95 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7246 (mmt180) REVERT: B 207 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: C 47 MET cc_start: 0.7674 (mtt) cc_final: 0.6764 (ptt) REVERT: C 95 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7484 (mmt180) REVERT: C 299 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8315 (mmm) outliers start: 16 outliers final: 10 residues processed: 121 average time/residue: 0.2391 time to fit residues: 45.3669 Evaluate side-chains 114 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1409 GLN Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1699 PHE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 143 optimal weight: 0.1980 chunk 150 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14523 Z= 0.166 Angle : 0.560 8.794 19687 Z= 0.264 Chirality : 0.042 0.137 2194 Planarity : 0.003 0.036 2528 Dihedral : 5.417 59.902 1997 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.05 % Allowed : 12.62 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.21), residues: 1765 helix: 1.09 (0.19), residues: 813 sheet: -0.42 (0.30), residues: 291 loop : -0.05 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.003 0.001 HIS C 88 PHE 0.010 0.001 PHE A 223 TYR 0.013 0.001 TYR D1255 ARG 0.003 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.766 Fit side-chains REVERT: A 192 ILE cc_start: 0.9396 (tp) cc_final: 0.9093 (tp) REVERT: A 305 MET cc_start: 0.8469 (mmm) cc_final: 0.8204 (mtp) REVERT: D 1699 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8123 (m-10) REVERT: D 1881 MET cc_start: 0.8857 (tmm) cc_final: 0.8481 (ppp) REVERT: B 95 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7273 (mmt180) REVERT: B 207 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: C 47 MET cc_start: 0.7651 (mtt) cc_final: 0.6779 (ptt) REVERT: C 95 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7485 (mmt180) REVERT: C 299 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8320 (mmm) outliers start: 16 outliers final: 11 residues processed: 119 average time/residue: 0.2450 time to fit residues: 45.7994 Evaluate side-chains 118 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1699 PHE Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 149 optimal weight: 0.0770 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14523 Z= 0.300 Angle : 0.613 9.172 19687 Z= 0.295 Chirality : 0.045 0.173 2194 Planarity : 0.004 0.036 2528 Dihedral : 5.590 60.356 1997 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.11 % Allowed : 12.69 % Favored : 86.20 % 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: 0.38 (0.21), residues: 1765 helix: 0.98 (0.19), residues: 818 sheet: -0.44 (0.30), residues: 291 loop : -0.17 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 340 HIS 0.003 0.001 HIS D1666 PHE 0.023 0.001 PHE D1776 TYR 0.012 0.001 TYR D1255 ARG 0.004 0.000 ARG B 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 192 ILE cc_start: 0.9420 (tp) cc_final: 0.9112 (tp) REVERT: D 1699 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8153 (m-10) REVERT: D 1881 MET cc_start: 0.8841 (tmm) cc_final: 0.8576 (tmm) REVERT: B 95 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7224 (mmt180) REVERT: C 47 MET cc_start: 0.7650 (mtt) cc_final: 0.6844 (ptt) REVERT: C 95 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7557 (mmt180) REVERT: C 299 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8387 (mmm) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.2494 time to fit residues: 44.3997 Evaluate side-chains 112 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1409 GLN Chi-restraints excluded: chain D residue 1656 ASP Chi-restraints excluded: chain D residue 1699 PHE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 299 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.0370 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 144 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.0470 chunk 123 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084315 restraints weight = 27005.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.083625 restraints weight = 15687.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084792 restraints weight = 11131.809| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14523 Z= 0.144 Angle : 0.565 10.271 19687 Z= 0.267 Chirality : 0.042 0.140 2194 Planarity : 0.003 0.033 2528 Dihedral : 5.294 54.755 1997 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.72 % Allowed : 13.21 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.21), residues: 1765 helix: 1.06 (0.19), residues: 816 sheet: -0.43 (0.30), residues: 291 loop : -0.06 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 340 HIS 0.003 0.001 HIS C 88 PHE 0.009 0.001 PHE A 223 TYR 0.012 0.001 TYR D1255 ARG 0.001 0.000 ARG D1491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.99 seconds wall clock time: 51 minutes 10.69 seconds (3070.69 seconds total)