Starting phenix.real_space_refine on Sun Oct 13 15:15:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fff_50355/10_2024/9fff_50355.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fff_50355/10_2024/9fff_50355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fff_50355/10_2024/9fff_50355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fff_50355/10_2024/9fff_50355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fff_50355/10_2024/9fff_50355.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fff_50355/10_2024/9fff_50355.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 67 5.16 5 C 9329 2.51 5 N 2726 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 15045 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 7054 Classifications: {'peptide': 1119} Incomplete info: {'backbone_only': 326, 'truncation_to_alanine': 147} Link IDs: {'PTRANS': 46, 'TRANS': 1072} Chain breaks: 10 Unresolved non-hydrogen bonds: 1877 Unresolved non-hydrogen angles: 2600 Unresolved non-hydrogen dihedrals: 1243 Unresolved non-hydrogen chiralities: 453 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 25, 'TRP:plan': 2, 'ASP:plan': 48, 'PHE:plan': 18, 'GLU:plan': 58, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 980 Chain: "B" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 6661 Classifications: {'peptide': 950} Incomplete info: {'backbone_only': 107, 'truncation_to_alanine': 136} Link IDs: {'PTRANS': 27, 'TRANS': 922} Chain breaks: 10 Unresolved non-hydrogen bonds: 873 Unresolved non-hydrogen angles: 1161 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 13, 'ASP:plan': 33, 'PHE:plan': 2, 'GLU:plan': 34, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 495 Chain: "S" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 657 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 673 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Time building chain proxies: 10.45, per 1000 atoms: 0.69 Number of scatterers: 15045 At special positions: 0 Unit cell: (101.475, 165.825, 137.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 63 15.00 O 2860 8.00 N 2726 7.00 C 9329 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.14 Conformation dependent library (CDL) restraints added in 2.1 seconds 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3108 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 2 sheets defined 78.5% alpha, 0.5% beta 21 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 91 through 108 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.633A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 163 removed outlier: 3.944A pdb=" N ALA A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 255 removed outlier: 4.094A pdb=" N ILE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 removed outlier: 4.014A pdb=" N ALA A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 removed outlier: 3.516A pdb=" N VAL A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 351 through 360 removed outlier: 3.820A pdb=" N GLN A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 376 removed outlier: 3.944A pdb=" N TRP A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.664A pdb=" N LEU A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 428 through 434 removed outlier: 3.846A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 4.370A pdb=" N LEU A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS A 447 " --> pdb=" O GLN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 469 through 486 Processing helix chain 'A' and resid 488 through 506 removed outlier: 3.602A pdb=" N ASP A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 removed outlier: 4.282A pdb=" N TYR A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 4.222A pdb=" N ILE A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 550 through 566 removed outlier: 3.564A pdb=" N GLN A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 removed outlier: 4.212A pdb=" N ILE A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.547A pdb=" N LEU A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 645 removed outlier: 4.494A pdb=" N LEU A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 659 through 668 Proline residue: A 665 - end of helix Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.137A pdb=" N SER A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 747 removed outlier: 3.519A pdb=" N GLU A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 771 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.789A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 802 removed outlier: 3.617A pdb=" N ASN A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 835 removed outlier: 4.035A pdb=" N LYS A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 Processing helix chain 'A' and resid 928 through 935 removed outlier: 4.029A pdb=" N VAL A 931 " --> pdb=" O ASP A 928 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 933 " --> pdb=" O GLU A 930 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 934 " --> pdb=" O VAL A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 979 removed outlier: 3.663A pdb=" N TRP A 973 " --> pdb=" O ASP A 969 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1005 Processing helix chain 'A' and resid 1007 through 1017 Processing helix chain 'A' and resid 1018 through 1036 removed outlier: 3.800A pdb=" N LEU A1022 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1072 removed outlier: 4.224A pdb=" N LEU A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1078 Processing helix chain 'A' and resid 1081 through 1097 removed outlier: 3.877A pdb=" N VAL A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A1092 " --> pdb=" O ALA A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1119 Processing helix chain 'A' and resid 1120 through 1122 No H-bonds generated for 'chain 'A' and resid 1120 through 1122' Processing helix chain 'A' and resid 1126 through 1141 Processing helix chain 'A' and resid 1146 through 1163 Processing helix chain 'A' and resid 1176 through 1193 removed outlier: 3.569A pdb=" N SER A1180 " --> pdb=" O SER A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1214 removed outlier: 4.770A pdb=" N VAL A1208 " --> pdb=" O SER A1204 " (cutoff:3.500A) Proline residue: A1209 - end of helix Processing helix chain 'A' and resid 1230 through 1248 removed outlier: 3.703A pdb=" N PHE A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1265 through 1285 removed outlier: 3.649A pdb=" N LYS A1283 " --> pdb=" O ILE A1279 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A1284 " --> pdb=" O ASN A1280 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A1285 " --> pdb=" O LEU A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1317 removed outlier: 4.577A pdb=" N MET A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) Proline residue: A1311 - end of helix removed outlier: 4.567A pdb=" N HIS A1315 " --> pdb=" O PRO A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1348 removed outlier: 4.389A pdb=" N GLN A1337 " --> pdb=" O LEU A1333 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS A1339 " --> pdb=" O THR A1335 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 Processing helix chain 'A' and resid 1356 through 1378 removed outlier: 3.581A pdb=" N LEU A1360 " --> pdb=" O HIS A1356 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A1372 " --> pdb=" O VAL A1368 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 224 Processing helix chain 'B' and resid 228 through 246 removed outlier: 4.175A pdb=" N GLU B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.998A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.589A pdb=" N LYS B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 removed outlier: 3.505A pdb=" N ILE B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.825A pdb=" N GLN B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.717A pdb=" N VAL B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 396 removed outlier: 3.603A pdb=" N GLU B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.592A pdb=" N PHE B 487 " --> pdb=" O THR B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.502A pdb=" N GLN B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 549 removed outlier: 3.962A pdb=" N ALA B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 595 removed outlier: 4.923A pdb=" N GLY B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 593 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 616 removed outlier: 4.112A pdb=" N MET B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR B 612 " --> pdb=" O TYR B 608 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 614 " --> pdb=" O GLY B 610 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 638 removed outlier: 3.840A pdb=" N TYR B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 666 through 684 Processing helix chain 'B' and resid 701 through 718 Processing helix chain 'B' and resid 736 through 764 removed outlier: 3.520A pdb=" N GLY B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 785 removed outlier: 3.513A pdb=" N CYS B 780 " --> pdb=" O GLY B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 821 Processing helix chain 'B' and resid 830 through 838 Processing helix chain 'B' and resid 838 through 859 removed outlier: 3.593A pdb=" N VAL B 846 " --> pdb=" O MET B 842 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA B 849 " --> pdb=" O ALA B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 891 removed outlier: 3.683A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG B 882 " --> pdb=" O CYS B 878 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 883 " --> pdb=" O LYS B 879 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 884 " --> pdb=" O ILE B 880 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 925 removed outlier: 3.741A pdb=" N CYS B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 919 " --> pdb=" O LEU B 915 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 937 removed outlier: 3.985A pdb=" N ASP B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 971 removed outlier: 3.604A pdb=" N LYS B 953 " --> pdb=" O ASN B 949 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER B 964 " --> pdb=" O GLN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 992 removed outlier: 3.775A pdb=" N LEU B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.705A pdb=" N LEU B1003 " --> pdb=" O SER B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1035 removed outlier: 3.527A pdb=" N PHE B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1056 Processing helix chain 'B' and resid 1075 through 1079 Processing helix chain 'B' and resid 1080 through 1085 removed outlier: 3.808A pdb=" N CYS B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1106 removed outlier: 3.809A pdb=" N TRP B1100 " --> pdb=" O GLU B1096 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B1101 " --> pdb=" O GLU B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1146 Processing helix chain 'B' and resid 1152 through 1177 removed outlier: 3.897A pdb=" N ASP B1156 " --> pdb=" O GLY B1152 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B1167 " --> pdb=" O SER B1163 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B1173 " --> pdb=" O LEU B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1202 Processing helix chain 'B' and resid 1202 through 1222 removed outlier: 3.763A pdb=" N ASN B1215 " --> pdb=" O THR B1211 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B1222 " --> pdb=" O SER B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1242 through 1250 Processing helix chain 'B' and resid 1251 through 1275 removed outlier: 4.240A pdb=" N ASN B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B1263 " --> pdb=" O ALA B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1294 through 1298 Processing sheet with id=AA1, first strand: chain 'A' and resid 685 through 687 Processing sheet with id=AA2, first strand: chain 'A' and resid 1385 through 1388 removed outlier: 3.665A pdb=" N TRP A1385 " --> pdb=" O ARG B1291 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 3123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4716 1.34 - 1.46: 2422 1.46 - 1.58: 8082 1.58 - 1.70: 126 1.70 - 1.82: 95 Bond restraints: 15441 Sorted by residual: bond pdb=" CA VAL A 273 " pdb=" CB VAL A 273 " ideal model delta sigma weight residual 1.539 1.524 0.015 5.40e-03 3.43e+04 8.17e+00 bond pdb=" N LYS A 400 " pdb=" CA LYS A 400 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.84e+00 bond pdb=" C VAL A1357 " pdb=" N PRO A1358 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.37e+00 bond pdb=" N SER A 393 " pdb=" CA SER A 393 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 6.02e+00 bond pdb=" N HIS A 392 " pdb=" CA HIS A 392 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.20e-02 6.94e+03 3.46e+00 ... (remaining 15436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 20827 2.42 - 4.84: 216 4.84 - 7.26: 43 7.26 - 9.69: 8 9.69 - 12.11: 3 Bond angle restraints: 21097 Sorted by residual: angle pdb=" CA MET A 270 " pdb=" CB MET A 270 " pdb=" CG MET A 270 " ideal model delta sigma weight residual 114.10 122.61 -8.51 2.00e+00 2.50e-01 1.81e+01 angle pdb=" C ILE A 391 " pdb=" N HIS A 392 " pdb=" CA HIS A 392 " ideal model delta sigma weight residual 120.54 115.16 5.38 1.35e+00 5.49e-01 1.59e+01 angle pdb=" N MET A 270 " pdb=" CA MET A 270 " pdb=" CB MET A 270 " ideal model delta sigma weight residual 110.28 115.80 -5.52 1.55e+00 4.16e-01 1.27e+01 angle pdb=" CA LEU A 792 " pdb=" CB LEU A 792 " pdb=" CG LEU A 792 " ideal model delta sigma weight residual 116.30 128.41 -12.11 3.50e+00 8.16e-02 1.20e+01 angle pdb=" CB MET B 392 " pdb=" CG MET B 392 " pdb=" SD MET B 392 " ideal model delta sigma weight residual 112.70 122.88 -10.18 3.00e+00 1.11e-01 1.15e+01 ... (remaining 21092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.99: 7797 32.99 - 65.99: 594 65.99 - 98.98: 45 98.98 - 131.98: 1 131.98 - 164.97: 1 Dihedral angle restraints: 8438 sinusoidal: 3245 harmonic: 5193 Sorted by residual: dihedral pdb=" C4' DC T 44 " pdb=" C3' DC T 44 " pdb=" O3' DC T 44 " pdb=" P DT T 45 " ideal model delta sinusoidal sigma weight residual 220.00 55.03 164.97 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA GLU B 790 " pdb=" C GLU B 790 " pdb=" N LYS B 791 " pdb=" CA LYS B 791 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG A1172 " pdb=" C ARG A1172 " pdb=" N GLU A1173 " pdb=" CA GLU A1173 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 8435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2215 0.082 - 0.165: 100 0.165 - 0.247: 2 0.247 - 0.329: 1 0.329 - 0.411: 1 Chirality restraints: 2319 Sorted by residual: chirality pdb=" CG LEU A1064 " pdb=" CB LEU A1064 " pdb=" CD1 LEU A1064 " pdb=" CD2 LEU A1064 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CG LEU B 590 " pdb=" CB LEU B 590 " pdb=" CD1 LEU B 590 " pdb=" CD2 LEU B 590 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE A1132 " pdb=" CA ILE A1132 " pdb=" CG1 ILE A1132 " pdb=" CG2 ILE A1132 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2316 not shown) Planarity restraints: 2556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 586 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.83e+00 pdb=" C CYS B 586 " 0.051 2.00e-02 2.50e+03 pdb=" O CYS B 586 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 587 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B1080 " -0.041 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO B1081 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B1081 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B1081 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 528 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO A 529 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 529 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 529 " -0.027 5.00e-02 4.00e+02 ... (remaining 2553 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 323 2.68 - 3.24: 16064 3.24 - 3.79: 24936 3.79 - 4.35: 30413 4.35 - 4.90: 46718 Nonbonded interactions: 118454 Sorted by model distance: nonbonded pdb=" OH TYR A 688 " pdb=" OG1 THR A 816 " model vdw 2.128 3.040 nonbonded pdb=" O ALA B1167 " pdb=" OG1 THR B1170 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASN B1075 " pdb=" OG1 THR B1078 " model vdw 2.169 3.040 nonbonded pdb=" O LEU A 927 " pdb=" NZ LYS A 974 " model vdw 2.178 3.120 nonbonded pdb=" O THR B1136 " pdb=" OG1 THR B1139 " model vdw 2.213 3.040 ... (remaining 118449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 42.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 0.045 15441 Z= 0.188 Angle : 0.646 12.107 21097 Z= 0.328 Chirality : 0.039 0.411 2319 Planarity : 0.004 0.063 2556 Dihedral : 20.681 164.971 5330 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 0.67 % Allowed : 33.05 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 2025 helix: 1.53 (0.14), residues: 1402 sheet: None (None), residues: 0 loop : -1.46 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1165 HIS 0.005 0.001 HIS A1061 PHE 0.028 0.001 PHE A1235 TYR 0.014 0.001 TYR A1297 ARG 0.005 0.000 ARG A1336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.598 Fit side-chains REVERT: A 394 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6720 (m) REVERT: A 1243 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 462 ILE cc_start: 0.9164 (pt) cc_final: 0.8878 (mm) REVERT: B 873 MET cc_start: 0.8129 (mmm) cc_final: 0.7609 (mmm) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.2541 time to fit residues: 43.1933 Evaluate side-chains 97 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain B residue 1281 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 0.0470 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN A1280 ASN A1332 GLN B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15441 Z= 0.213 Angle : 0.619 8.821 21097 Z= 0.321 Chirality : 0.040 0.251 2319 Planarity : 0.004 0.061 2556 Dihedral : 19.572 164.338 2864 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.84 % Favored : 95.11 % Rotamer: Outliers : 4.21 % Allowed : 30.78 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2025 helix: 1.47 (0.14), residues: 1465 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1008 HIS 0.004 0.001 HIS B1175 PHE 0.031 0.001 PHE A1067 TYR 0.016 0.001 TYR A1297 ARG 0.003 0.000 ARG A1336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 100 time to evaluate : 1.721 Fit side-chains REVERT: A 732 LEU cc_start: 0.4388 (OUTLIER) cc_final: 0.3980 (mm) REVERT: A 736 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.6055 (t80) REVERT: A 1243 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 705 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.9083 (m-10) REVERT: B 1086 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7999 (pp) REVERT: B 1154 CYS cc_start: 0.7399 (OUTLIER) cc_final: 0.5836 (t) outliers start: 50 outliers final: 22 residues processed: 145 average time/residue: 0.2200 time to fit residues: 54.2088 Evaluate side-chains 120 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 923 TYR Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 921 MET Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1154 CYS Chi-restraints excluded: chain B residue 1281 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 192 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1325 GLN A1339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15441 Z= 0.258 Angle : 0.633 9.402 21097 Z= 0.326 Chirality : 0.040 0.224 2319 Planarity : 0.004 0.057 2556 Dihedral : 19.617 164.418 2857 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.97 % Allowed : 30.11 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 2025 helix: 1.40 (0.14), residues: 1478 sheet: None (None), residues: 0 loop : -1.82 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1268 HIS 0.003 0.001 HIS B1269 PHE 0.018 0.002 PHE A1131 TYR 0.019 0.002 TYR A1297 ARG 0.004 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 94 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.4161 (mm) REVERT: A 736 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.6175 (t80) REVERT: A 1243 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 429 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8922 (pp) REVERT: B 462 ILE cc_start: 0.9141 (pt) cc_final: 0.8918 (mm) REVERT: B 705 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.9128 (m-10) REVERT: B 1086 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8077 (pp) outliers start: 71 outliers final: 43 residues processed: 155 average time/residue: 0.2292 time to fit residues: 59.2827 Evaluate side-chains 138 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 90 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 923 TYR Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1150 ARG Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 828 HIS Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 1061 GLN Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1175 HIS Chi-restraints excluded: chain B residue 1260 ILE Chi-restraints excluded: chain B residue 1281 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.0020 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 ASN B1201 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15441 Z= 0.173 Angle : 0.599 10.905 21097 Z= 0.300 Chirality : 0.039 0.244 2319 Planarity : 0.004 0.059 2556 Dihedral : 19.527 161.375 2857 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.05 % Allowed : 31.79 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 2025 helix: 1.59 (0.14), residues: 1477 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1148 HIS 0.004 0.001 HIS A1340 PHE 0.015 0.001 PHE A1131 TYR 0.018 0.001 TYR A1297 ARG 0.003 0.000 ARG B1160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 105 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 584 MET cc_start: 0.7952 (mpp) cc_final: 0.7552 (mtm) REVERT: A 736 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5932 (t80) REVERT: A 1150 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.5460 (ptm-80) REVERT: B 462 ILE cc_start: 0.9090 (pt) cc_final: 0.8831 (mm) REVERT: B 716 MET cc_start: 0.9200 (mmp) cc_final: 0.8689 (mmm) REVERT: B 842 MET cc_start: 0.7515 (mmt) cc_final: 0.7281 (mmp) REVERT: B 873 MET cc_start: 0.8089 (mmm) cc_final: 0.7776 (mmm) REVERT: B 1170 THR cc_start: 0.7280 (OUTLIER) cc_final: 0.6950 (t) outliers start: 60 outliers final: 31 residues processed: 154 average time/residue: 0.2343 time to fit residues: 60.5764 Evaluate side-chains 128 residues out of total 1873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 923 TYR Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1148 TRP Chi-restraints excluded: chain A residue 1150 ARG Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1310 MET Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1342 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 921 MET Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1175 HIS Chi-restraints excluded: chain B residue 1281 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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-5477/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-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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: 55.2575 > 50: distance: 46 - 65: 3.920 distance: 50 - 71: 7.118 distance: 55 - 79: 10.908 distance: 66 - 67: 4.732 distance: 67 - 68: 8.635 distance: 67 - 71: 4.842 distance: 69 - 70: 5.563 distance: 71 - 72: 7.894 distance: 72 - 73: 8.931 distance: 72 - 75: 6.352 distance: 73 - 74: 15.599 distance: 73 - 79: 9.592 distance: 75 - 76: 7.042 distance: 76 - 77: 5.140 distance: 76 - 78: 3.765 distance: 79 - 80: 8.095 distance: 80 - 81: 7.254 distance: 80 - 83: 10.579 distance: 81 - 82: 6.502 distance: 81 - 89: 5.212 distance: 83 - 84: 24.980 distance: 84 - 85: 11.219 distance: 84 - 86: 10.414 distance: 85 - 87: 12.161 distance: 86 - 88: 7.212 distance: 87 - 88: 10.175 distance: 89 - 90: 9.872 distance: 90 - 91: 22.591 distance: 90 - 93: 24.951 distance: 91 - 92: 14.882 distance: 91 - 96: 8.020 distance: 93 - 94: 6.570 distance: 93 - 95: 34.136 distance: 96 - 97: 12.462 distance: 97 - 98: 16.338 distance: 97 - 100: 13.399 distance: 98 - 99: 6.345 distance: 98 - 104: 18.075 distance: 100 - 101: 11.873 distance: 101 - 102: 15.022 distance: 101 - 103: 30.603 distance: 104 - 105: 3.454 distance: 105 - 106: 8.952 distance: 105 - 108: 8.183 distance: 106 - 107: 11.750 distance: 106 - 116: 11.316 distance: 108 - 109: 11.338 distance: 109 - 110: 10.433 distance: 109 - 111: 15.328 distance: 110 - 112: 7.243 distance: 111 - 113: 6.422 distance: 112 - 114: 13.404 distance: 113 - 114: 8.310 distance: 114 - 115: 7.221 distance: 116 - 117: 4.473 distance: 117 - 118: 3.836 distance: 117 - 120: 7.421 distance: 118 - 119: 6.047 distance: 118 - 125: 18.960 distance: 120 - 121: 16.192 distance: 121 - 122: 9.557 distance: 122 - 123: 9.908 distance: 123 - 124: 14.972 distance: 125 - 126: 15.181 distance: 126 - 127: 25.735 distance: 126 - 129: 14.437 distance: 127 - 128: 11.936 distance: 127 - 131: 20.678 distance: 129 - 130: 18.982 distance: 131 - 132: 20.344 distance: 131 - 137: 28.469 distance: 132 - 133: 15.642 distance: 132 - 135: 30.191 distance: 133 - 134: 10.563 distance: 133 - 138: 13.238 distance: 134 - 158: 10.342 distance: 135 - 136: 36.652 distance: 136 - 137: 22.587 distance: 138 - 139: 14.450 distance: 139 - 140: 6.402 distance: 139 - 142: 14.386 distance: 140 - 141: 9.875 distance: 140 - 145: 16.858 distance: 141 - 165: 27.791 distance: 142 - 143: 11.080 distance: 142 - 144: 19.256