Starting phenix.real_space_refine on Sun Mar 17 21:22:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw4_13674/03_2024/7pw4_13674_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw4_13674/03_2024/7pw4_13674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw4_13674/03_2024/7pw4_13674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw4_13674/03_2024/7pw4_13674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw4_13674/03_2024/7pw4_13674_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw4_13674/03_2024/7pw4_13674_updated.pdb" } resolution = 3.27 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= 0.005 sd= 0.076 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 94 5.16 5 Cl 1 4.86 5 C 12188 2.51 5 N 3359 2.21 5 O 3313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A ASP 2209": "OD1" <-> "OD2" Residue "A GLU 3655": "OE1" <-> "OE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 514": "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: 18965 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1944, 13719 Classifications: {'peptide': 1944} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 537} Link IDs: {'PTRANS': 61, 'TRANS': 1882} Chain breaks: 39 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1536 Unresolved non-hydrogen angles: 2021 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 3, 'ASN:plan1': 17, 'TYR:plan': 4, 'UNK:plan-1': 195, 'TRP:plan': 4, 'ASP:plan': 47, 'PHE:plan': 6, 'GLU:plan': 70, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 912 Chain: "B" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2718 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "C" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2421 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'88C': 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: 1 residue: pdb="MG MG C 602 " occ=0.00 Time building chain proxies: 9.61, per 1000 atoms: 0.51 Number of scatterers: 18965 At special positions: 0 Unit cell: (120.87, 127.68, 182.157, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 94 16.00 P 9 15.00 Mg 1 11.99 O 3313 8.00 N 3359 7.00 C 12188 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: 8.50 Conformation dependent library (CDL) restraints added in 3.6 seconds 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 5 sheets defined 65.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.776A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.516A pdb=" N UNK A 171 " --> pdb=" O UNK A 167 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N UNK A 173 " --> pdb=" O UNK A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 208 through 220 removed outlier: 4.256A pdb=" N UNK A 220 " --> pdb=" O UNK A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.627A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.912A pdb=" N UNK A 284 " --> pdb=" O UNK A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.987A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.673A 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: 4.115A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 429 through 443 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 476 through 488 removed outlier: 3.665A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.910A pdb=" N ILE A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 558 through 582 removed outlier: 4.056A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' 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: 3.831A pdb=" N THR A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.942A 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: 3.756A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A 675 " --> pdb=" O HIS A 671 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 676 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 678 " --> pdb=" O ARG A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 702 No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 725 through 742 Processing helix chain 'A' and resid 749 through 752 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 805 Processing helix chain 'A' and resid 812 through 822 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 870 Processing helix chain 'A' and resid 882 through 889 Processing helix chain 'A' and resid 903 through 907 removed outlier: 4.113A pdb=" N LYS A 907 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 926 Processing helix chain 'A' and resid 936 through 955 removed outlier: 4.002A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 998 removed outlier: 4.069A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.899A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 4.515A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.079A 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 1069 through 1082 Processing helix chain 'A' and resid 1086 through 1098 removed outlier: 3.954A pdb=" N SER A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1115 removed outlier: 3.863A pdb=" N ASN A1108 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1133 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1180 through 1196 Processing helix chain 'A' and resid 1200 through 1217 Processing helix chain 'A' and resid 1228 through 1239 Processing helix chain 'A' and resid 1242 through 1251 removed outlier: 3.540A pdb=" N GLU A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 3.945A 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 1318 through 1340 removed outlier: 3.883A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A1332 " --> pdb=" O SER A1328 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Proline residue: A1334 - end of helix removed outlier: 3.540A pdb=" N THR A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1366 removed outlier: 3.608A pdb=" N SER A1365 " --> pdb=" O GLU A1361 " (cutoff:3.500A) 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 1382 Processing helix chain 'A' and resid 1391 through 1409 removed outlier: 3.875A pdb=" N GLN A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.517A 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: 3.555A 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 1513 removed outlier: 4.069A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 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 1589 through 1591 No H-bonds generated for 'chain 'A' and resid 1589 through 1591' Processing helix chain 'A' and resid 1596 through 1611 removed outlier: 4.159A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1636 Processing helix chain 'A' and resid 1647 through 1655 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.579A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1716 Processing helix chain 'A' and resid 1729 through 1741 removed outlier: 3.569A pdb=" N ASP A1738 " --> pdb=" O ARG A1734 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A1739 " --> pdb=" O LYS A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1758 removed outlier: 3.727A pdb=" N ASN A1758 " --> pdb=" O PHE A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1798 removed outlier: 3.526A pdb=" N MET A1787 " --> pdb=" O ASP A1783 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A1788 " --> pdb=" O MET A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1810 removed outlier: 3.864A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1836 through 1849 Processing helix chain 'A' and resid 1857 through 1864 Processing helix chain 'A' and resid 1925 through 1939 removed outlier: 4.029A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1957 Processing helix chain 'A' and resid 1963 through 1977 Processing helix chain 'A' and resid 2007 through 2020 Processing helix chain 'A' and resid 2037 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 2161 through 2177 removed outlier: 3.549A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2183 removed outlier: 3.819A pdb=" N GLN A2183 " --> pdb=" O ILE A2180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2180 through 2183' Processing helix chain 'A' and resid 2214 through 2231 Processing helix chain 'A' and resid 2249 through 2264 removed outlier: 3.545A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2277 through 2288 Processing helix chain 'A' and resid 2297 through 2303 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 2362 through 2364 No H-bonds generated for 'chain 'A' and resid 2362 through 2364' Processing helix chain 'A' and resid 2377 through 2383 removed outlier: 3.641A 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 3643 Processing helix chain 'A' and resid 3647 through 3650 No H-bonds generated for 'chain 'A' and resid 3647 through 3650' Processing helix chain 'A' and resid 3655 through 3657 No H-bonds generated for 'chain 'A' and resid 3655 through 3657' Processing helix chain 'B' and resid 8 through 11 No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.588A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 205 removed outlier: 3.577A pdb=" N SER B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 removed outlier: 3.802A pdb=" N PHE B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY B 232 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 238 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.905A pdb=" N LYS B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 296 through 314 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 410 through 422 removed outlier: 4.254A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.816A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 484 removed outlier: 3.803A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 Proline residue: B 505 - end of helix Processing helix chain 'B' and resid 524 through 538 Processing helix chain 'B' and resid 544 through 558 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 298 through 314 Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 381 through 395 removed outlier: 3.513A pdb=" N GLN C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 454 through 456 No H-bonds generated for 'chain 'C' and resid 454 through 456' 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 517 Processing sheet with id= A, first strand: chain 'A' and resid 2129 through 2131 removed outlier: 3.849A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A2152 " --> pdb=" O LEU A2140 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2211 through 2213 Processing sheet with id= C, first strand: chain 'B' and resid 336 through 339 removed outlier: 9.083A pdb=" N TYR B 337 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 267 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 339 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE B 269 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLY B 54 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.260A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 317 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU C 210 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE C 319 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS C 366 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL C 320 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 368 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLN C 322 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 370 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.634A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2979 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: 7.07 Time building geometry restraints manager: 9.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2960 1.30 - 1.43: 4915 1.43 - 1.56: 11281 1.56 - 1.69: 12 1.69 - 1.82: 143 Bond restraints: 19311 Sorted by residual: bond pdb=" CA LEU A 741 " pdb=" C LEU A 741 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.37e-02 5.33e+03 3.39e+01 bond pdb=" C LYS A 744 " pdb=" O LYS A 744 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.17e-02 7.31e+03 2.75e+01 bond pdb=" C LEU A 741 " pdb=" O LEU A 741 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.32e-02 5.74e+03 2.66e+01 bond pdb=" C28 88C A3702 " pdb=" N30 88C A3702 " ideal model delta sigma weight residual 1.352 1.453 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C ARG A 743 " pdb=" O ARG A 743 " ideal model delta sigma weight residual 1.235 1.171 0.065 1.34e-02 5.57e+03 2.32e+01 ... (remaining 19306 not shown) Histogram of bond angle deviations from ideal: 99.29 - 107.40: 662 107.40 - 115.52: 11960 115.52 - 123.64: 13255 123.64 - 131.75: 446 131.75 - 139.87: 44 Bond angle restraints: 26367 Sorted by residual: angle pdb=" CA PRO A1392 " pdb=" N PRO A1392 " pdb=" CD PRO A1392 " ideal model delta sigma weight residual 112.00 103.82 8.18 1.40e+00 5.10e-01 3.41e+01 angle pdb=" O07 88C A3702 " pdb=" S06 88C A3702 " pdb=" O08 88C A3702 " ideal model delta sigma weight residual 117.67 101.03 16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.20 108.01 5.19 9.60e-01 1.09e+00 2.92e+01 angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 111.02 117.32 -6.30 1.25e+00 6.40e-01 2.54e+01 angle pdb=" N GLN C 213 " pdb=" CA GLN C 213 " pdb=" C GLN C 213 " ideal model delta sigma weight residual 111.03 115.78 -4.75 1.11e+00 8.12e-01 1.83e+01 ... (remaining 26362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 11272 34.64 - 69.28: 211 69.28 - 103.91: 18 103.91 - 138.55: 2 138.55 - 173.19: 3 Dihedral angle restraints: 11506 sinusoidal: 3792 harmonic: 7714 Sorted by residual: dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -109.11 173.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -129.71 -169.39 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C6 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 61.05 -82.07 143.12 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 11503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 3232 0.990 - 1.980: 0 1.980 - 2.969: 0 2.969 - 3.959: 0 3.959 - 4.949: 3 Chirality restraints: 3235 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.43 -4.95 2.00e-01 2.50e+01 6.12e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.38 4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.50 4.81 2.00e-01 2.50e+01 5.79e+02 ... (remaining 3232 not shown) Planarity restraints: 3282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1391 " 0.092 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO A1392 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO A1392 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A1392 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 740 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C VAL A 740 " -0.062 2.00e-02 2.50e+03 pdb=" O VAL A 740 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU A 741 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 395 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 396 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.027 5.00e-02 4.00e+02 ... (remaining 3279 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 81 2.60 - 3.18: 16010 3.18 - 3.75: 28701 3.75 - 4.33: 36345 4.33 - 4.90: 63051 Nonbonded interactions: 144188 Sorted by model distance: nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 2.030 2.170 nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 2.064 2.170 nonbonded pdb=" OE1 GLN A1126 " pdb=" OH TYR A1194 " model vdw 2.100 2.440 nonbonded pdb=" OH TYR A 669 " pdb=" OE1 GLU A 737 " model vdw 2.208 2.440 nonbonded pdb=" OH TYR A2193 " pdb=" O ILE A2353 " model vdw 2.236 2.440 ... (remaining 144183 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.010 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: 12.770 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 54.240 Find NCS groups from input model: 0.650 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 19311 Z= 0.214 Angle : 0.622 16.645 26367 Z= 0.335 Chirality : 0.153 4.949 3235 Planarity : 0.004 0.134 3282 Dihedral : 14.412 173.191 6440 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 1.69 (0.19), residues: 2355 helix: 2.45 (0.14), residues: 1472 sheet: -0.28 (0.46), residues: 129 loop : -1.43 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2221 HIS 0.003 0.001 HIS A2337 PHE 0.025 0.001 PHE C 325 TYR 0.016 0.001 TYR A 998 ARG 0.005 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: A 1950 MET cc_start: 0.7108 (tmm) cc_final: 0.6423 (tmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2645 time to fit residues: 79.6191 Evaluate side-chains 141 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 110 optimal weight: 0.0030 chunk 67 optimal weight: 0.0570 chunk 133 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 0.0030 chunk 237 optimal weight: 4.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 HIS A1854 HIS ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19311 Z= 0.114 Angle : 0.447 11.838 26367 Z= 0.210 Chirality : 0.035 0.333 3235 Planarity : 0.004 0.074 3282 Dihedral : 8.610 125.454 2854 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.59 % Allowed : 5.95 % Favored : 93.46 % 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 (0.19), residues: 2355 helix: 2.50 (0.14), residues: 1484 sheet: -0.09 (0.47), residues: 129 loop : -1.34 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 415 HIS 0.008 0.000 HIS A 581 PHE 0.014 0.001 PHE A 405 TYR 0.014 0.001 TYR A 998 ARG 0.004 0.000 ARG C 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: A 1465 HIS cc_start: 0.6695 (m-70) cc_final: 0.6445 (m-70) REVERT: A 1950 MET cc_start: 0.7096 (tmm) cc_final: 0.6807 (tmm) REVERT: A 2375 MET cc_start: 0.8315 (tpt) cc_final: 0.7860 (tpt) outliers start: 10 outliers final: 7 residues processed: 157 average time/residue: 0.2812 time to fit residues: 71.9172 Evaluate side-chains 147 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 236 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS A2337 HIS B 159 ASN ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19311 Z= 0.166 Angle : 0.443 8.486 26367 Z= 0.214 Chirality : 0.036 0.277 3235 Planarity : 0.004 0.064 3282 Dihedral : 8.401 122.086 2854 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.12 % Allowed : 8.19 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2355 helix: 2.46 (0.14), residues: 1480 sheet: -0.13 (0.45), residues: 129 loop : -1.30 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1095 HIS 0.007 0.001 HIS A1551 PHE 0.016 0.001 PHE A 405 TYR 0.014 0.001 TYR A 998 ARG 0.006 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 2.165 Fit side-chains REVERT: A 1950 MET cc_start: 0.7123 (tmm) cc_final: 0.6800 (tmm) REVERT: B 415 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.6917 (t60) REVERT: C 517 ARG cc_start: 0.7548 (ptt-90) cc_final: 0.6986 (ptt-90) outliers start: 19 outliers final: 12 residues processed: 150 average time/residue: 0.2789 time to fit residues: 68.0752 Evaluate side-chains 150 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 226 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19311 Z= 0.134 Angle : 0.416 8.224 26367 Z= 0.202 Chirality : 0.035 0.280 3235 Planarity : 0.003 0.061 3282 Dihedral : 8.226 119.728 2854 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.53 % Allowed : 9.36 % Favored : 89.10 % 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 (0.18), residues: 2355 helix: 2.47 (0.14), residues: 1480 sheet: -0.08 (0.45), residues: 129 loop : -1.26 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1629 HIS 0.005 0.001 HIS A1551 PHE 0.010 0.001 PHE B 188 TYR 0.013 0.001 TYR A 998 ARG 0.002 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 2.275 Fit side-chains revert: symmetry clash REVERT: A 1950 MET cc_start: 0.7112 (tmm) cc_final: 0.6778 (tmm) REVERT: B 415 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.6894 (t60) REVERT: C 517 ARG cc_start: 0.7579 (ptt-90) cc_final: 0.6940 (ptt-90) outliers start: 26 outliers final: 18 residues processed: 155 average time/residue: 0.2808 time to fit residues: 70.5916 Evaluate side-chains 152 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1074 MET Chi-restraints excluded: chain A residue 1551 HIS Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 3 optimal weight: 50.0000 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 129 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19311 Z= 0.241 Angle : 0.481 8.551 26367 Z= 0.236 Chirality : 0.037 0.252 3235 Planarity : 0.004 0.061 3282 Dihedral : 8.181 117.210 2854 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.41 % Allowed : 10.66 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2355 helix: 2.30 (0.14), residues: 1482 sheet: -0.18 (0.45), residues: 129 loop : -1.40 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A2207 HIS 0.033 0.001 HIS A1551 PHE 0.017 0.001 PHE A1827 TYR 0.014 0.001 TYR A 998 ARG 0.002 0.000 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 2.124 Fit side-chains REVERT: A 405 PHE cc_start: 0.8996 (t80) cc_final: 0.8707 (t80) REVERT: A 1950 MET cc_start: 0.7205 (tmm) cc_final: 0.6825 (tmm) REVERT: B 415 TRP cc_start: 0.8186 (OUTLIER) cc_final: 0.7002 (t60) REVERT: C 517 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.6920 (ptt-90) outliers start: 24 outliers final: 18 residues processed: 147 average time/residue: 0.2829 time to fit residues: 68.1664 Evaluate side-chains 149 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1732 VAL Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.6980 chunk 228 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 253 optimal weight: 0.0020 chunk 210 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 0.0980 chunk 133 optimal weight: 30.0000 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1551 HIS ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19311 Z= 0.119 Angle : 0.417 8.847 26367 Z= 0.204 Chirality : 0.035 0.235 3235 Planarity : 0.003 0.058 3282 Dihedral : 7.941 114.663 2854 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 12.07 % Favored : 86.81 % 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 (0.18), residues: 2355 helix: 2.43 (0.14), residues: 1481 sheet: -0.04 (0.46), residues: 129 loop : -1.29 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1629 HIS 0.002 0.000 HIS A 706 PHE 0.009 0.001 PHE A 364 TYR 0.013 0.001 TYR A 998 ARG 0.010 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 2.235 Fit side-chains REVERT: A 405 PHE cc_start: 0.8993 (t80) cc_final: 0.8768 (t80) REVERT: A 1950 MET cc_start: 0.7191 (tmm) cc_final: 0.6825 (tmm) REVERT: B 415 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.6842 (t60) REVERT: C 517 ARG cc_start: 0.7548 (ptt-90) cc_final: 0.6929 (ptt-90) outliers start: 19 outliers final: 14 residues processed: 140 average time/residue: 0.2780 time to fit residues: 64.5222 Evaluate side-chains 142 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3631 MET Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 284 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 0.5980 chunk 28 optimal weight: 0.0000 chunk 144 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 252 optimal weight: 0.0000 chunk 158 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 ASN A1551 HIS ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19311 Z= 0.113 Angle : 0.409 9.736 26367 Z= 0.199 Chirality : 0.034 0.203 3235 Planarity : 0.003 0.057 3282 Dihedral : 7.619 110.063 2854 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.18 % Allowed : 11.96 % Favored : 86.87 % 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: 1.90 (0.18), residues: 2355 helix: 2.53 (0.14), residues: 1484 sheet: 0.04 (0.46), residues: 129 loop : -1.27 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1629 HIS 0.002 0.000 HIS A 706 PHE 0.008 0.001 PHE A 364 TYR 0.014 0.001 TYR A 998 ARG 0.001 0.000 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 2.123 Fit side-chains REVERT: A 403 ARG cc_start: 0.8743 (mmt180) cc_final: 0.8484 (tmm160) REVERT: A 1950 MET cc_start: 0.7187 (tmm) cc_final: 0.6835 (tmm) REVERT: B 415 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.6841 (t60) outliers start: 20 outliers final: 14 residues processed: 147 average time/residue: 0.2778 time to fit residues: 66.6577 Evaluate side-chains 144 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1782 ASP Chi-restraints excluded: chain A residue 1946 LEU Chi-restraints excluded: chain A residue 2127 THR Chi-restraints excluded: chain A residue 2154 PHE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 415 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 512 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.705 > 50: distance: 31 - 33: 25.867 distance: 33 - 34: 10.004 distance: 34 - 35: 18.154 distance: 35 - 36: 15.012 distance: 35 - 37: 16.111 distance: 37 - 38: 5.421 distance: 38 - 39: 7.981 distance: 38 - 41: 27.113 distance: 39 - 40: 10.280 distance: 39 - 44: 9.174 distance: 41 - 42: 15.479 distance: 41 - 43: 11.771 distance: 44 - 45: 9.461 distance: 45 - 48: 9.896 distance: 46 - 47: 4.650 distance: 46 - 52: 11.258 distance: 48 - 49: 13.845 distance: 48 - 50: 9.778 distance: 49 - 51: 15.488 distance: 52 - 53: 8.045 distance: 52 - 119: 5.475 distance: 53 - 54: 5.890 distance: 53 - 56: 4.976 distance: 54 - 55: 12.448 distance: 54 - 59: 13.460 distance: 55 - 116: 22.578 distance: 56 - 57: 19.783 distance: 56 - 58: 4.153 distance: 59 - 60: 5.093 distance: 60 - 61: 22.047 distance: 60 - 63: 17.088 distance: 61 - 62: 28.432 distance: 61 - 67: 21.175 distance: 63 - 64: 14.892 distance: 63 - 65: 12.111 distance: 64 - 66: 10.338 distance: 67 - 68: 34.232 distance: 67 - 105: 33.008 distance: 68 - 69: 13.893 distance: 68 - 71: 11.322 distance: 69 - 70: 11.218 distance: 69 - 75: 25.448 distance: 71 - 72: 24.348 distance: 72 - 73: 18.423 distance: 72 - 74: 28.871 distance: 75 - 76: 10.311 distance: 75 - 81: 20.698 distance: 76 - 77: 9.324 distance: 76 - 79: 16.560 distance: 77 - 78: 32.592 distance: 77 - 82: 20.934 distance: 79 - 80: 16.255 distance: 80 - 81: 18.773 distance: 82 - 83: 18.039 distance: 83 - 84: 5.374 distance: 83 - 86: 28.469 distance: 84 - 85: 6.268 distance: 84 - 87: 16.004 distance: 87 - 88: 24.458 distance: 88 - 89: 7.777 distance: 88 - 91: 14.128 distance: 89 - 90: 6.251 distance: 89 - 92: 17.547 distance: 92 - 93: 6.446 distance: 93 - 94: 16.686 distance: 93 - 96: 24.486 distance: 94 - 95: 33.861 distance: 94 - 97: 10.675