Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 22:31:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlq_33285/07_2023/7xlq_33285_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlq_33285/07_2023/7xlq_33285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlq_33285/07_2023/7xlq_33285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlq_33285/07_2023/7xlq_33285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlq_33285/07_2023/7xlq_33285_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlq_33285/07_2023/7xlq_33285_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.103 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 Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13081 2.51 5 N 3274 2.21 5 O 3662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A ARG 781": "NH1" <-> "NH2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A ARG 1249": "NH1" <-> "NH2" Residue "A ARG 1261": "NH1" <-> "NH2" Residue "A TYR 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1347": "OE1" <-> "OE2" Residue "A GLU 1372": "OE1" <-> "OE2" Residue "A GLU 1398": "OE1" <-> "OE2" Residue "A GLU 1556": "OE1" <-> "OE2" Residue "A ARG 1647": "NH1" <-> "NH2" Residue "A GLU 1679": "OE1" <-> "OE2" Residue "A GLU 1727": "OE1" <-> "OE2" Residue "A ARG 1731": "NH1" <-> "NH2" Residue "A GLU 1743": "OE1" <-> "OE2" Residue "A GLU 1834": "OE1" <-> "OE2" Residue "A GLU 1838": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D GLU 597": "OE1" <-> "OE2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D GLU 747": "OE1" <-> "OE2" Residue "D GLU 757": "OE1" <-> "OE2" Residue "D ARG 831": "NH1" <-> "NH2" Residue "D GLU 877": "OE1" <-> "OE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 20132 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10674 Classifications: {'peptide': 1319} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1278} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 7637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7637 Classifications: {'peptide': 955} Link IDs: {'PTRANS': 42, 'TRANS': 912} Chain breaks: 3 Chain: "B" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1259 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 332 Unusual residues: {' CA': 1, '3PE': 1, 'R16': 7, 'Y01': 6} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {' CA': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 9.59, per 1000 atoms: 0.48 Number of scatterers: 20132 At special positions: 0 Unit cell: (176.8, 114.4, 183.04, 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) Ca 2 19.99 S 112 16.00 P 1 15.00 O 3662 8.00 N 3274 7.00 C 13081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A1318 " - pdb=" SG CYS A1329 " distance=2.02 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1694 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 354 " - pdb=" SG CYS D1059 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN D 895 " " NAG D1201 " - " ASN D 604 " " NAG D1202 " - " ASN D 613 " " NAG D1203 " - " ASN D 675 " " NAG D1204 " - " ASN D 888 " " NAG D1205 " - " ASN D 184 " " NAG D1207 " - " ASN D 92 " " NAG D1208 " - " ASN D 324 " " NAG D1209 " - " ASN D 348 " " NAG E 1 " - " ASN D 468 " " NAG F 1 " - " ASN D 824 " Time building additional restraints: 8.37 Conformation dependent library (CDL) restraints added in 2.7 seconds 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 17 sheets defined 53.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.565A pdb=" N TYR A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.698A pdb=" N ILE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 127 through 146 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 175 removed outlier: 4.049A pdb=" N MET A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.599A pdb=" N SER A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 218 removed outlier: 3.660A pdb=" N GLN A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.554A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.805A pdb=" N PHE A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.834A pdb=" N VAL A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 339 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.516A pdb=" N LEU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 386 removed outlier: 3.950A pdb=" N ALA A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.675A pdb=" N LEU A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.753A pdb=" N TRP A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.512A pdb=" N VAL A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 526 removed outlier: 3.539A pdb=" N HIS A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 560 removed outlier: 3.509A pdb=" N GLY A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 3.511A pdb=" N LEU A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.694A pdb=" N LEU A 589 " --> pdb=" O TYR A 585 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.528A pdb=" N VAL A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 removed outlier: 3.632A pdb=" N MET A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 669 removed outlier: 3.630A pdb=" N VAL A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 removed outlier: 3.794A pdb=" N ALA A 680 " --> pdb=" O MET A 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 680' Processing helix chain 'A' and resid 681 through 689 removed outlier: 3.884A pdb=" N THR A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.550A pdb=" N ALA A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 721 removed outlier: 4.119A pdb=" N GLN A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 776 through 785 Processing helix chain 'A' and resid 1144 through 1146 No H-bonds generated for 'chain 'A' and resid 1144 through 1146' Processing helix chain 'A' and resid 1147 through 1152 removed outlier: 4.133A pdb=" N ASN A1151 " --> pdb=" O HIS A1147 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1152 " --> pdb=" O TYR A1148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1147 through 1152' Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 3.640A pdb=" N CYS A1158 " --> pdb=" O TYR A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1172 removed outlier: 3.723A pdb=" N ALA A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1207 removed outlier: 3.600A pdb=" N TYR A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A1191 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1243 removed outlier: 3.878A pdb=" N LEU A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.819A pdb=" N ILE A1254 " --> pdb=" O ASP A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 Proline residue: A1265 - end of helix Processing helix chain 'A' and resid 1267 through 1272 removed outlier: 3.848A pdb=" N ARG A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1287 removed outlier: 3.593A pdb=" N CYS A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 Processing helix chain 'A' and resid 1307 through 1312 Processing helix chain 'A' and resid 1357 through 1370 removed outlier: 3.598A pdb=" N LEU A1365 " --> pdb=" O ALA A1361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A1368 " --> pdb=" O THR A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1383 removed outlier: 3.621A pdb=" N HIS A1380 " --> pdb=" O GLN A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1400 removed outlier: 3.508A pdb=" N SER A1400 " --> pdb=" O MET A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1410 removed outlier: 3.567A pdb=" N PHE A1407 " --> pdb=" O TYR A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1425 removed outlier: 3.795A pdb=" N ASN A1416 " --> pdb=" O PHE A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1438 Processing helix chain 'A' and resid 1441 through 1447 Processing helix chain 'A' and resid 1467 through 1476 removed outlier: 5.568A pdb=" N HIS A1473 " --> pdb=" O TYR A1469 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A1474 " --> pdb=" O ARG A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1491 Processing helix chain 'A' and resid 1505 through 1526 removed outlier: 3.906A pdb=" N VAL A1520 " --> pdb=" O ALA A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1533 Processing helix chain 'A' and resid 1533 through 1538 Processing helix chain 'A' and resid 1543 through 1560 removed outlier: 3.597A pdb=" N ILE A1548 " --> pdb=" O ILE A1544 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1550 " --> pdb=" O ASP A1546 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A1555 " --> pdb=" O ILE A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1574 removed outlier: 4.271A pdb=" N PHE A1574 " --> pdb=" O ASN A1571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1571 through 1574' Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 4.112A pdb=" N ARG A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1590 removed outlier: 3.689A pdb=" N ARG A1588 " --> pdb=" O LYS A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1603 Processing helix chain 'A' and resid 1609 through 1630 removed outlier: 3.734A pdb=" N ILE A1614 " --> pdb=" O VAL A1610 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A1615 " --> pdb=" O CYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1661 removed outlier: 3.514A pdb=" N LEU A1655 " --> pdb=" O GLY A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1671 Processing helix chain 'A' and resid 1698 through 1723 Processing helix chain 'A' and resid 1725 through 1730 Processing helix chain 'A' and resid 1737 through 1740 Processing helix chain 'A' and resid 1741 through 1753 removed outlier: 3.643A pdb=" N VAL A1745 " --> pdb=" O LEU A1741 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A1749 " --> pdb=" O VAL A1745 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1750 " --> pdb=" O ARG A1746 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR A1751 " --> pdb=" O VAL A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1771 removed outlier: 3.505A pdb=" N GLU A1766 " --> pdb=" O THR A1762 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1768 " --> pdb=" O MET A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1793 removed outlier: 4.061A pdb=" N ARG A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A1790 " --> pdb=" O ALA A1786 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A1791 " --> pdb=" O TYR A1787 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1817 Processing helix chain 'A' and resid 1825 through 1843 removed outlier: 4.040A pdb=" N GLN A1829 " --> pdb=" O GLY A1825 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A1834 " --> pdb=" O GLN A1830 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A1839 " --> pdb=" O LEU A1835 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A1841 " --> pdb=" O LYS A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1855 Processing helix chain 'A' and resid 1864 through 1871 Processing helix chain 'D' and resid 29 through 52 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 74 through 110 Processing helix chain 'D' and resid 134 through 138 removed outlier: 3.543A pdb=" N ASP D 137 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 138' Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 4.000A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.506A pdb=" N VAL D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.739A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.660A pdb=" N PHE D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.846A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 431 removed outlier: 4.225A pdb=" N ASN D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 639 through 646 Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 675 through 689 removed outlier: 3.553A pdb=" N ARG D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 719 removed outlier: 3.793A pdb=" N ILE D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.601A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 770 " --> pdb=" O ARG D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 Processing helix chain 'D' and resid 866 through 871 Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 890 removed outlier: 4.180A pdb=" N MET D 883 " --> pdb=" O ASP D 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.614A pdb=" N LEU B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 removed outlier: 3.705A pdb=" N LYS B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 366 through 379 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 393 through 412 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 253 Processing sheet with id=AA2, first strand: chain 'A' and resid 1316 through 1318 Processing sheet with id=AA3, first strand: chain 'A' and resid 1332 through 1335 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 142 through 144 removed outlier: 9.120A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.654A pdb=" N ARG D 157 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 215 through 217 removed outlier: 3.567A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 215 through 217 removed outlier: 3.567A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 298 through 300 Processing sheet with id=AB1, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.179A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR D 409 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 511 through 513 Processing sheet with id=AB3, first strand: chain 'D' and resid 592 through 593 Processing sheet with id=AB4, first strand: chain 'D' and resid 729 through 736 removed outlier: 3.770A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 800 through 802 Processing sheet with id=AB6, first strand: chain 'D' and resid 859 through 862 removed outlier: 7.180A pdb=" N LEU D 859 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP D 854 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 849 " --> pdb=" O VAL D1018 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D1018 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 892 through 904 removed outlier: 3.681A pdb=" N PHE D 982 " --> pdb=" O ALA D 893 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.984A pdb=" N SER B 265 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASP B 322 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR B 267 " --> pdb=" O ASP B 322 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 232 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 233 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE B 344 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 235 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 341 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 389 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR B 343 " --> pdb=" O LEU B 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 884 hydrogen bonds defined for protein. 2481 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: 7.58 Time building geometry restraints manager: 8.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3220 1.32 - 1.45: 5615 1.45 - 1.58: 11570 1.58 - 1.71: 2 1.71 - 1.84: 181 Bond restraints: 20588 Sorted by residual: bond pdb=" C TYR A 682 " pdb=" O TYR A 682 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.16e-02 7.43e+03 1.85e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C PRO D 529 " pdb=" O PRO D 529 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 9.79e+00 bond pdb=" N PRO D 529 " pdb=" CA PRO D 529 " ideal model delta sigma weight residual 1.469 1.429 0.040 1.28e-02 6.10e+03 9.57e+00 bond pdb=" N ILE A1620 " pdb=" CA ILE A1620 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.03e+00 ... (remaining 20583 not shown) Histogram of bond angle deviations from ideal: 94.46 - 102.40: 94 102.40 - 110.34: 4845 110.34 - 118.27: 10940 118.27 - 126.21: 11717 126.21 - 134.14: 280 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N SER A1479 " pdb=" CA SER A1479 " pdb=" C SER A1479 " ideal model delta sigma weight residual 114.09 101.02 13.07 1.55e+00 4.16e-01 7.11e+01 angle pdb=" CA CYS D 697 " pdb=" CB CYS D 697 " pdb=" SG CYS D 697 " ideal model delta sigma weight residual 114.40 130.54 -16.14 2.30e+00 1.89e-01 4.92e+01 angle pdb=" C GLY A 272 " pdb=" N CYS A 273 " pdb=" CA CYS A 273 " ideal model delta sigma weight residual 120.39 128.41 -8.02 1.39e+00 5.18e-01 3.33e+01 angle pdb=" CA CYS D 667 " pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " ideal model delta sigma weight residual 114.40 126.92 -12.52 2.30e+00 1.89e-01 2.96e+01 angle pdb=" N ILE A1294 " pdb=" CA ILE A1294 " pdb=" C ILE A1294 " ideal model delta sigma weight residual 111.90 107.78 4.12 8.10e-01 1.52e+00 2.58e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 11313 23.74 - 47.49: 717 47.49 - 71.23: 77 71.23 - 94.97: 16 94.97 - 118.71: 1 Dihedral angle restraints: 12124 sinusoidal: 4991 harmonic: 7133 Sorted by residual: dihedral pdb=" CB CYS A 268 " pdb=" SG CYS A 268 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual 93.00 -177.66 -89.34 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 7.69 85.31 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA THR A 182 " pdb=" C THR A 182 " pdb=" N HIS A 183 " pdb=" CA HIS A 183 " ideal model delta harmonic sigma weight residual -180.00 -139.38 -40.62 0 5.00e+00 4.00e-02 6.60e+01 ... (remaining 12121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2712 0.068 - 0.137: 413 0.137 - 0.205: 27 0.205 - 0.274: 11 0.274 - 0.342: 3 Chirality restraints: 3166 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3163 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 204 " 0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO A 205 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 200 " -0.059 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO D 201 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 201 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 201 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 284 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO A 285 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.036 5.00e-02 4.00e+02 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 387 2.67 - 3.23: 19958 3.23 - 3.79: 29940 3.79 - 4.34: 43561 4.34 - 4.90: 69952 Nonbonded interactions: 163798 Sorted by model distance: nonbonded pdb=" O ASP D 596 " pdb=" OD1 ASP D 596 " model vdw 2.117 3.040 nonbonded pdb=" OD1 ASN D 481 " pdb=" O6 NAG E 1 " model vdw 2.177 2.440 nonbonded pdb=" O GLN D 528 " pdb=" NE2 GLN D 901 " model vdw 2.211 2.520 nonbonded pdb=" OH TYR D 410 " pdb=" OE2 GLU D 412 " model vdw 2.215 2.440 nonbonded pdb=" OE2 GLU A1556 " pdb=" NH1 ARG A1579 " model vdw 2.252 2.520 ... (remaining 163793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.670 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 51.820 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.006 0.076 20588 Z= 0.396 Angle : 0.854 16.137 27876 Z= 0.492 Chirality : 0.051 0.342 3166 Planarity : 0.005 0.096 3470 Dihedral : 14.857 118.715 7481 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.92 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.52 (0.16), residues: 2414 helix: -2.51 (0.13), residues: 1187 sheet: -2.08 (0.32), residues: 244 loop : -1.91 (0.19), residues: 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 277 time to evaluate : 2.017 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 283 average time/residue: 0.3056 time to fit residues: 135.1739 Evaluate side-chains 235 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.950 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.1685 time to fit residues: 4.0759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN A1354 HIS A1641 ASN ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 GLN D 482 GLN D 509 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20588 Z= 0.220 Angle : 0.657 9.527 27876 Z= 0.345 Chirality : 0.044 0.215 3166 Planarity : 0.005 0.071 3470 Dihedral : 7.946 109.610 2802 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.42 % Favored : 92.54 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.48 (0.16), residues: 2414 helix: -1.45 (0.14), residues: 1237 sheet: -1.59 (0.31), residues: 251 loop : -1.69 (0.20), residues: 926 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 268 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 282 average time/residue: 0.3181 time to fit residues: 141.6045 Evaluate side-chains 251 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 4 residues processed: 16 average time/residue: 0.1961 time to fit residues: 9.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 237 optimal weight: 50.0000 chunk 196 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 176 optimal weight: 0.0040 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN A1354 HIS ** A1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN ** D1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 20588 Z= 0.247 Angle : 0.630 11.212 27876 Z= 0.324 Chirality : 0.044 0.276 3166 Planarity : 0.004 0.058 3470 Dihedral : 7.647 108.536 2802 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.71 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.17), residues: 2414 helix: -0.87 (0.14), residues: 1235 sheet: -1.45 (0.31), residues: 251 loop : -1.55 (0.21), residues: 928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4828 Ramachandran restraints generated. 2414 Oldfield, 0 Emsley, 2414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 283 average time/residue: 0.3079 time to fit residues: 139.1647 Evaluate side-chains 258 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 4 residues processed: 18 average time/residue: 0.1991 time to fit residues: 9.8615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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-1.21rc1-5013/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: 50.4605 > 50: distance: 58 - 70: 25.603 distance: 70 - 71: 19.148 distance: 71 - 72: 41.170 distance: 71 - 74: 32.714 distance: 72 - 73: 28.768 distance: 72 - 77: 13.066 distance: 74 - 75: 17.351 distance: 74 - 76: 11.279 distance: 77 - 78: 15.237 distance: 78 - 79: 15.333 distance: 78 - 81: 10.698 distance: 79 - 80: 24.407 distance: 79 - 83: 21.437 distance: 80 - 104: 37.400 distance: 81 - 82: 13.078 distance: 83 - 84: 6.471 distance: 84 - 85: 19.687 distance: 84 - 87: 13.095 distance: 85 - 86: 7.498 distance: 85 - 88: 14.467 distance: 86 - 113: 9.726 distance: 88 - 89: 13.986 distance: 89 - 90: 50.054 distance: 89 - 92: 24.636 distance: 90 - 91: 10.221 distance: 90 - 96: 32.021 distance: 91 - 120: 32.319 distance: 92 - 93: 29.100 distance: 93 - 94: 11.668 distance: 96 - 97: 24.969 distance: 97 - 98: 36.058 distance: 97 - 100: 13.538 distance: 98 - 99: 24.965 distance: 98 - 104: 42.184 distance: 99 - 131: 18.910 distance: 100 - 101: 12.643 distance: 101 - 102: 8.776 distance: 101 - 103: 11.066 distance: 104 - 105: 18.163 distance: 105 - 106: 12.916 distance: 105 - 108: 16.032 distance: 106 - 107: 10.602 distance: 106 - 113: 11.508 distance: 107 - 140: 8.334 distance: 108 - 109: 11.656 distance: 109 - 110: 17.798 distance: 110 - 111: 14.384 distance: 110 - 112: 11.617 distance: 113 - 114: 12.315 distance: 114 - 115: 16.606 distance: 114 - 117: 9.465 distance: 115 - 116: 28.758 distance: 115 - 120: 20.756 distance: 116 - 149: 17.028 distance: 117 - 118: 6.518 distance: 117 - 119: 17.844 distance: 120 - 121: 5.273 distance: 121 - 122: 35.824 distance: 121 - 124: 9.171 distance: 122 - 123: 25.524 distance: 122 - 131: 32.371 distance: 123 - 157: 9.511 distance: 124 - 125: 21.936 distance: 125 - 126: 19.475 distance: 125 - 127: 11.895 distance: 126 - 128: 24.081 distance: 127 - 129: 23.572 distance: 128 - 130: 20.511 distance: 129 - 130: 17.337 distance: 131 - 132: 24.596 distance: 132 - 133: 36.812 distance: 132 - 135: 27.313 distance: 133 - 134: 18.321 distance: 133 - 140: 19.575 distance: 134 - 163: 14.359 distance: 135 - 136: 17.111 distance: 136 - 137: 12.158 distance: 137 - 138: 17.533 distance: 138 - 139: 3.683 distance: 140 - 141: 16.254 distance: 141 - 142: 9.384 distance: 141 - 144: 6.459 distance: 142 - 143: 6.044 distance: 142 - 149: 6.629 distance: 143 - 170: 10.475 distance: 144 - 145: 25.651 distance: 145 - 146: 38.226 distance: 146 - 147: 29.778 distance: 147 - 148: 26.884