Starting phenix.real_space_refine on Sun Mar 17 02:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw9_13679/03_2024/7pw9_13679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw9_13679/03_2024/7pw9_13679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw9_13679/03_2024/7pw9_13679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw9_13679/03_2024/7pw9_13679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw9_13679/03_2024/7pw9_13679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw9_13679/03_2024/7pw9_13679_updated.pdb" } resolution = 3.12 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= 0.003 sd= 0.101 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 12 5.49 5 Mg 1 5.21 5 S 80 5.16 5 C 10472 2.51 5 N 2882 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "C TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16339 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1952, 13831 Classifications: {'peptide': 1952} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 530} Link IDs: {'PTRANS': 62, 'TRANS': 1889} Chain breaks: 37 Unresolved non-hydrogen bonds: 1489 Unresolved non-hydrogen angles: 1951 Unresolved non-hydrogen dihedrals: 1074 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 2, 'ASN:plan1': 17, 'TYR:plan': 4, 'UNK:plan-1': 195, 'TRP:plan': 3, 'ASP:plan': 46, 'PHE:plan': 5, 'GLU:plan': 70, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 890 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2409 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ANP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 IHP A3702 " occ=0.00 ... (34 atoms not shown) pdb=" P6 IHP A3702 " occ=0.00 residue: pdb="MG MG C 602 " occ=0.00 Time building chain proxies: 9.11, per 1000 atoms: 0.56 Number of scatterers: 16339 At special positions: 0 Unit cell: (131.085, 114.061, 180.454, 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 80 16.00 P 12 15.00 Mg 1 11.99 O 2892 8.00 N 2882 7.00 C 10472 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 3.0 seconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 3 sheets defined 69.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.884A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.888A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N UNK A 173 " --> pdb=" O UNK A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.266A pdb=" N UNK A 220 " --> pdb=" O UNK A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.779A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.605A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.611A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.701A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 529 through 535 removed outlier: 4.395A pdb=" N TYR A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 558 through 583 removed outlier: 4.239A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 604 through 622 removed outlier: 3.958A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 653 through 656 No H-bonds generated for 'chain 'A' and resid 653 through 656' Processing helix chain 'A' and resid 658 through 678 removed outlier: 3.802A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS A 675 " --> pdb=" O HIS A 671 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N HIS A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE A 678 " --> pdb=" O ARG A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 removed outlier: 5.121A pdb=" N LYS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 725 through 743 removed outlier: 3.841A pdb=" N ARG A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 755 through 767 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 792 through 806 removed outlier: 3.860A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.672A pdb=" N LYS A 819 " --> pdb=" O GLN A 815 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 836 through 850 Processing helix chain 'A' and resid 859 through 871 Processing helix chain 'A' and resid 882 through 889 removed outlier: 3.561A pdb=" N LEU A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 909 through 926 Processing helix chain 'A' and resid 938 through 955 Processing helix chain 'A' and resid 970 through 998 removed outlier: 3.675A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 984 " --> pdb=" O LEU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.509A pdb=" N PHE A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 4.683A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1068 through 1082 removed outlier: 3.779A pdb=" N THR A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1098 removed outlier: 3.908A pdb=" N SER A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1115 Processing helix chain 'A' and resid 1118 through 1133 removed outlier: 3.566A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1150 removed outlier: 3.637A pdb=" N LEU A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1196 Processing helix chain 'A' and resid 1200 through 1215 Processing helix chain 'A' and resid 1228 through 1239 Processing helix chain 'A' and resid 1243 through 1251 removed outlier: 3.888A pdb=" N LEU A1251 " --> pdb=" O GLU A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1304 Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1333 through 1340 Processing helix chain 'A' and resid 1348 through 1366 Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1391 through 1409 removed outlier: 3.969A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.546A pdb=" N ARG A1435 " --> pdb=" O PHE A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1449 Processing helix chain 'A' and resid 1459 through 1466 removed outlier: 3.590A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1494 Processing helix chain 'A' and resid 1497 through 1512 Processing helix chain 'A' and resid 1519 through 1534 Processing helix chain 'A' and resid 1540 through 1550 Processing helix chain 'A' and resid 1560 through 1569 Processing helix chain 'A' and resid 1587 through 1590 No H-bonds generated for 'chain 'A' and resid 1587 through 1590' Processing helix chain 'A' and resid 1596 through 1611 removed outlier: 3.928A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1636 removed outlier: 3.606A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1655 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.716A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1715 Processing helix chain 'A' and resid 1729 through 1740 Processing helix chain 'A' and resid 1742 through 1757 Processing helix chain 'A' and resid 1782 through 1798 Processing helix chain 'A' and resid 1804 through 1812 removed outlier: 4.224A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A1812 " --> pdb=" O GLU A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1831 removed outlier: 3.668A pdb=" N LEU A1830 " --> pdb=" O LEU A1826 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN A1831 " --> pdb=" O PHE A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1849 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1858 through 1864 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.689A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1962 through 1977 Processing helix chain 'A' and resid 2007 through 2019 Processing helix chain 'A' and resid 2036 through 2043 Processing helix chain 'A' and resid 2047 through 2055 Processing helix chain 'A' and resid 2069 through 2082 Processing helix chain 'A' and resid 2092 through 2095 No H-bonds generated for 'chain 'A' and resid 2092 through 2095' Processing helix chain 'A' and resid 2161 through 2177 removed outlier: 3.598A pdb=" N PHE A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2183 Processing helix chain 'A' and resid 2214 through 2231 removed outlier: 3.508A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2262 Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2277 through 2290 Processing helix chain 'A' and resid 2295 through 2303 removed outlier: 3.560A pdb=" N GLU A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2331 Processing helix chain 'A' and resid 2338 through 2340 No H-bonds generated for 'chain 'A' and resid 2338 through 2340' Processing helix chain 'A' and resid 2361 through 2363 No H-bonds generated for 'chain 'A' and resid 2361 through 2363' Processing helix chain 'A' and resid 2377 through 2383 removed outlier: 3.964A pdb=" N LEU A2383 " --> pdb=" O ILE A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2405 Processing helix chain 'A' and resid 2407 through 2418 Processing helix chain 'A' and resid 3608 through 3621 Processing helix chain 'A' and resid 3633 through 3645 Processing helix chain 'A' and resid 3647 through 3652 removed outlier: 3.656A pdb=" N GLN A3652 " --> pdb=" O ASP A3648 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 243 through 246 No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 296 through 314 Processing helix chain 'C' and resid 330 through 337 Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 466 through 478 Processing helix chain 'C' and resid 492 through 507 Processing helix chain 'C' and resid 511 through 518 Processing sheet with id= A, first strand: chain 'A' and resid 2195 through 2197 removed outlier: 3.512A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2341 through 2343 Processing sheet with id= C, first strand: chain 'C' and resid 428 through 432 removed outlier: 8.832A pdb=" N PHE C 429 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE C 369 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL C 431 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 371 " --> pdb=" O VAL C 431 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 317 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 321 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL C 209 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 270 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 269 " --> pdb=" O ASP C 257 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE C 258 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS C 182 " --> pdb=" O PHE C 258 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2760 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: 7.09 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2561 1.30 - 1.43: 4216 1.43 - 1.56: 9714 1.56 - 1.69: 17 1.69 - 1.81: 126 Bond restraints: 16634 Sorted by residual: bond pdb=" O3A ANP A3701 " pdb=" PB ANP A3701 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" CA LEU A 741 " pdb=" C LEU A 741 " ideal model delta sigma weight residual 1.522 1.440 0.082 1.39e-02 5.18e+03 3.50e+01 bond pdb=" N3B ANP A3701 " pdb=" PG ANP A3701 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C LEU A 741 " pdb=" O LEU A 741 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.32e-02 5.74e+03 1.95e+01 bond pdb=" C MET A 742 " pdb=" O MET A 742 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.35e-02 5.49e+03 1.69e+01 ... (remaining 16629 not shown) Histogram of bond angle deviations from ideal: 100.40 - 108.27: 693 108.27 - 116.15: 10452 116.15 - 124.02: 11180 124.02 - 131.90: 370 131.90 - 139.77: 43 Bond angle restraints: 22738 Sorted by residual: angle pdb=" PB ANP A3701 " pdb=" N3B ANP A3701 " pdb=" PG ANP A3701 " ideal model delta sigma weight residual 126.95 110.42 16.53 3.00e+00 1.11e-01 3.04e+01 angle pdb=" N LYS A 744 " pdb=" CA LYS A 744 " pdb=" C LYS A 744 " ideal model delta sigma weight residual 111.28 115.80 -4.52 1.09e+00 8.42e-01 1.72e+01 angle pdb=" N THR A 747 " pdb=" CA THR A 747 " pdb=" C THR A 747 " ideal model delta sigma weight residual 111.75 116.59 -4.84 1.28e+00 6.10e-01 1.43e+01 angle pdb=" O1B ANP A3701 " pdb=" PB ANP A3701 " pdb=" O2B ANP A3701 " ideal model delta sigma weight residual 120.08 109.11 10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" N ILE A2353 " pdb=" CA ILE A2353 " pdb=" C ILE A2353 " ideal model delta sigma weight residual 109.34 116.31 -6.97 2.08e+00 2.31e-01 1.12e+01 ... (remaining 22733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.40: 9676 33.40 - 66.80: 221 66.80 - 100.19: 19 100.19 - 133.59: 8 133.59 - 166.99: 3 Dihedral angle restraints: 9927 sinusoidal: 3286 harmonic: 6641 Sorted by residual: dihedral pdb=" C6 IHP A3702 " pdb=" C1 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" O12 IHP A3702 " ideal model delta sinusoidal sigma weight residual 61.05 -105.94 166.99 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C4 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" O12 IHP A3702 " ideal model delta sinusoidal sigma weight residual 60.90 -157.33 -141.77 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O12 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" O13 IHP A3702 " ideal model delta sinusoidal sigma weight residual 64.08 -73.04 137.12 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 9924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 2804 1.003 - 2.005: 0 2.005 - 3.008: 0 3.008 - 4.011: 0 4.011 - 5.013: 3 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C2 IHP A3702 " pdb=" C1 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" O12 IHP A3702 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C4 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" C5 IHP A3702 " pdb=" O14 IHP A3702 " both_signs ideal model delta sigma weight residual False 2.48 -2.41 4.89 2.00e-01 2.50e+01 5.98e+02 chirality pdb=" C1 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" C6 IHP A3702 " pdb=" O11 IHP A3702 " both_signs ideal model delta sigma weight residual False 2.32 -2.45 4.76 2.00e-01 2.50e+01 5.68e+02 ... (remaining 2804 not shown) Planarity restraints: 2823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A2258 " 0.031 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A2259 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2259 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2259 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 740 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C VAL A 740 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 740 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 741 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 742 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C MET A 742 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 742 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 743 " -0.011 2.00e-02 2.50e+03 ... (remaining 2820 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 83 2.60 - 3.17: 13783 3.17 - 3.75: 25058 3.75 - 4.32: 31853 4.32 - 4.90: 54830 Nonbonded interactions: 125607 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.021 2.170 nonbonded pdb=" O1A ATP C 601 " pdb="MG MG C 602 " model vdw 2.021 2.170 nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 2.029 2.170 nonbonded pdb=" O3A ATP C 601 " pdb="MG MG C 602 " model vdw 2.059 2.170 nonbonded pdb=" O TYR A 888 " pdb=" OG SER C 479 " model vdw 2.177 2.440 ... (remaining 125602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.960 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 48.880 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.142 16634 Z= 0.222 Angle : 0.672 16.532 22738 Z= 0.350 Chirality : 0.165 5.013 2807 Planarity : 0.004 0.048 2823 Dihedral : 15.149 166.991 5565 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % 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: 1.77 (0.20), residues: 2008 helix: 2.49 (0.15), residues: 1281 sheet: -0.65 (0.53), residues: 81 loop : -1.42 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1629 HIS 0.003 0.001 HIS A2352 PHE 0.013 0.001 PHE C 466 TYR 0.018 0.001 TYR C 299 ARG 0.004 0.000 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.858 Fit side-chains REVERT: A 368 MET cc_start: 0.5259 (ptm) cc_final: 0.4672 (tmm) REVERT: A 1857 LEU cc_start: 0.8295 (tp) cc_final: 0.8030 (tp) REVERT: A 2326 MET cc_start: 0.8672 (mmp) cc_final: 0.8317 (mmp) REVERT: A 2345 MET cc_start: 0.8110 (mmt) cc_final: 0.7881 (mmt) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.2829 time to fit residues: 84.3655 Evaluate side-chains 160 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.0070 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 68 optimal weight: 0.0010 chunk 107 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 overall best weight: 0.9608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1758 ASN A2122 HIS C 233 GLN C 322 GLN C 397 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16634 Z= 0.170 Angle : 0.489 12.129 22738 Z= 0.232 Chirality : 0.037 0.316 2807 Planarity : 0.003 0.045 2823 Dihedral : 9.221 113.872 2475 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 0.88 % Allowed : 6.97 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 2008 helix: 2.63 (0.15), residues: 1285 sheet: -0.14 (0.58), residues: 79 loop : -1.33 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1629 HIS 0.013 0.001 HIS C 397 PHE 0.013 0.001 PHE C 466 TYR 0.019 0.001 TYR A 998 ARG 0.001 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.720 Fit side-chains REVERT: A 368 MET cc_start: 0.4902 (ptm) cc_final: 0.4700 (tmm) REVERT: A 2326 MET cc_start: 0.8682 (mmp) cc_final: 0.8170 (mmp) REVERT: A 2345 MET cc_start: 0.8151 (mmt) cc_final: 0.7834 (mmt) outliers start: 13 outliers final: 10 residues processed: 170 average time/residue: 0.2746 time to fit residues: 71.1156 Evaluate side-chains 166 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1835 VAL Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN C 397 HIS C 399 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16634 Z= 0.150 Angle : 0.461 8.955 22738 Z= 0.220 Chirality : 0.036 0.299 2807 Planarity : 0.003 0.044 2823 Dihedral : 8.790 107.949 2473 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 1.02 % Allowed : 9.48 % Favored : 89.51 % 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: 2.08 (0.20), residues: 2008 helix: 2.67 (0.15), residues: 1288 sheet: 0.18 (0.59), residues: 81 loop : -1.28 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1629 HIS 0.008 0.001 HIS C 397 PHE 0.013 0.001 PHE C 466 TYR 0.018 0.001 TYR A 998 ARG 0.002 0.000 ARG A3629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.764 Fit side-chains revert: symmetry clash REVERT: A 2326 MET cc_start: 0.8667 (mmp) cc_final: 0.8217 (mmp) REVERT: A 2345 MET cc_start: 0.8145 (mmt) cc_final: 0.7810 (mmt) outliers start: 15 outliers final: 12 residues processed: 171 average time/residue: 0.2739 time to fit residues: 72.8911 Evaluate side-chains 163 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.2980 chunk 153 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 0.0040 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2122 HIS A2192 HIS C 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16634 Z= 0.197 Angle : 0.490 9.135 22738 Z= 0.237 Chirality : 0.037 0.268 2807 Planarity : 0.003 0.043 2823 Dihedral : 8.436 101.778 2473 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 1.42 % Allowed : 11.98 % 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: 1.97 (0.20), residues: 2008 helix: 2.58 (0.15), residues: 1285 sheet: 0.30 (0.60), residues: 81 loop : -1.33 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3657 HIS 0.005 0.001 HIS A2352 PHE 0.014 0.001 PHE C 466 TYR 0.020 0.001 TYR A 998 ARG 0.003 0.000 ARG A3629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.652 Fit side-chains revert: symmetry clash REVERT: A 1352 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7978 (tt) REVERT: A 2345 MET cc_start: 0.8164 (mmt) cc_final: 0.7803 (mmt) outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 0.2583 time to fit residues: 66.5339 Evaluate side-chains 162 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1389 ASP Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 185 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2122 HIS C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16634 Z= 0.185 Angle : 0.476 9.546 22738 Z= 0.230 Chirality : 0.037 0.273 2807 Planarity : 0.003 0.043 2823 Dihedral : 8.306 97.943 2473 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.69 % Allowed : 12.73 % Favored : 85.58 % 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: 1.96 (0.20), residues: 2008 helix: 2.56 (0.15), residues: 1284 sheet: 0.31 (0.60), residues: 81 loop : -1.31 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A3657 HIS 0.004 0.001 HIS A2352 PHE 0.013 0.001 PHE C 466 TYR 0.019 0.001 TYR A 998 ARG 0.003 0.000 ARG A3629 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 1352 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7955 (tt) outliers start: 25 outliers final: 16 residues processed: 173 average time/residue: 0.2691 time to fit residues: 72.9046 Evaluate side-chains 167 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 2.9990 chunk 195 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2122 HIS C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16634 Z= 0.141 Angle : 0.465 12.837 22738 Z= 0.222 Chirality : 0.036 0.238 2807 Planarity : 0.003 0.043 2823 Dihedral : 7.952 89.690 2473 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 1.49 % Allowed : 13.07 % Favored : 85.44 % 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: 2.10 (0.20), residues: 2008 helix: 2.65 (0.15), residues: 1286 sheet: 0.40 (0.60), residues: 81 loop : -1.22 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1629 HIS 0.003 0.000 HIS A2352 PHE 0.012 0.001 PHE C 466 TYR 0.017 0.001 TYR A 998 ARG 0.002 0.000 ARG A3629 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.805 Fit side-chains revert: symmetry clash REVERT: A 1352 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7923 (tt) REVERT: A 2326 MET cc_start: 0.8565 (mmp) cc_final: 0.8219 (mmp) outliers start: 22 outliers final: 18 residues processed: 170 average time/residue: 0.2912 time to fit residues: 78.0180 Evaluate side-chains 171 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 2248 ARG Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1758 ASN A2122 HIS A2161 HIS C 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16634 Z= 0.225 Angle : 0.525 12.258 22738 Z= 0.251 Chirality : 0.038 0.274 2807 Planarity : 0.004 0.043 2823 Dihedral : 7.449 76.857 2473 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 1.49 % Allowed : 14.56 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 2008 helix: 2.43 (0.15), residues: 1288 sheet: 0.33 (0.61), residues: 81 loop : -1.36 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A3657 HIS 0.004 0.001 HIS A 650 PHE 0.014 0.001 PHE C 466 TYR 0.021 0.001 TYR A 998 ARG 0.003 0.000 ARG A3629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 1352 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8048 (tt) outliers start: 22 outliers final: 17 residues processed: 173 average time/residue: 0.2540 time to fit residues: 68.4156 Evaluate side-chains 171 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 7.9990 chunk 86 optimal weight: 0.0770 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2122 HIS C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16634 Z= 0.126 Angle : 0.473 14.047 22738 Z= 0.221 Chirality : 0.036 0.281 2807 Planarity : 0.003 0.044 2823 Dihedral : 7.041 72.631 2473 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 1.29 % Allowed : 15.10 % Favored : 83.62 % 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: 2.04 (0.20), residues: 2008 helix: 2.61 (0.15), residues: 1286 sheet: 0.43 (0.63), residues: 79 loop : -1.25 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1629 HIS 0.003 0.000 HIS A2122 PHE 0.012 0.001 PHE C 466 TYR 0.016 0.001 TYR A 998 ARG 0.003 0.000 ARG A3629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.695 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 167 average time/residue: 0.2572 time to fit residues: 67.2639 Evaluate side-chains 169 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 2248 ARG Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.0040 chunk 189 optimal weight: 1.9990 chunk 202 optimal weight: 0.0970 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 191 optimal weight: 0.0030 chunk 201 optimal weight: 0.0040 chunk 132 optimal weight: 20.0000 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2122 HIS C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16634 Z= 0.119 Angle : 0.468 13.254 22738 Z= 0.220 Chirality : 0.035 0.272 2807 Planarity : 0.003 0.044 2823 Dihedral : 6.620 71.881 2473 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 1.29 % Allowed : 15.57 % Favored : 83.14 % 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: 2.17 (0.20), residues: 2008 helix: 2.65 (0.15), residues: 1297 sheet: 0.55 (0.63), residues: 79 loop : -1.14 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2098 HIS 0.003 0.000 HIS A2352 PHE 0.012 0.001 PHE C 466 TYR 0.016 0.001 TYR A 998 ARG 0.003 0.000 ARG A3629 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 2345 MET cc_start: 0.8203 (mmt) cc_final: 0.7736 (mmt) outliers start: 19 outliers final: 16 residues processed: 171 average time/residue: 0.2586 time to fit residues: 69.6484 Evaluate side-chains 170 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 2248 ARG Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 0.0070 chunk 130 optimal weight: 30.0000 chunk 101 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2122 HIS C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16634 Z= 0.135 Angle : 0.490 15.348 22738 Z= 0.229 Chirality : 0.036 0.246 2807 Planarity : 0.003 0.044 2823 Dihedral : 6.482 71.211 2473 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 1.15 % Allowed : 16.11 % Favored : 82.74 % 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: 2.16 (0.20), residues: 2008 helix: 2.63 (0.15), residues: 1294 sheet: 0.62 (0.62), residues: 81 loop : -1.12 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2098 HIS 0.003 0.000 HIS A2352 PHE 0.012 0.001 PHE C 466 TYR 0.017 0.001 TYR A 998 ARG 0.003 0.000 ARG A3629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 2345 MET cc_start: 0.8183 (mmt) cc_final: 0.7763 (mmt) outliers start: 17 outliers final: 15 residues processed: 164 average time/residue: 0.2638 time to fit residues: 66.7107 Evaluate side-chains 171 residues out of total 1843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2209 ASP Chi-restraints excluded: chain A residue 2248 ARG Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 178 optimal weight: 0.7980 chunk 74 optimal weight: 0.0270 chunk 183 optimal weight: 0.0370 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2122 HIS C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.182523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145615 restraints weight = 22443.981| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.48 r_work: 0.3558 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16634 Z= 0.118 Angle : 0.474 14.073 22738 Z= 0.221 Chirality : 0.035 0.249 2807 Planarity : 0.003 0.044 2823 Dihedral : 6.228 69.477 2473 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 1.02 % Allowed : 16.11 % Favored : 82.87 % 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: 2.24 (0.20), residues: 2008 helix: 2.66 (0.15), residues: 1300 sheet: 0.65 (0.62), residues: 81 loop : -1.04 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2098 HIS 0.003 0.000 HIS A2352 PHE 0.011 0.001 PHE C 466 TYR 0.016 0.001 TYR C 299 ARG 0.003 0.000 ARG A3629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.11 seconds wall clock time: 62 minutes 31.96 seconds (3751.96 seconds total)