Starting phenix.real_space_refine on Sat Aug 23 22:53:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fff_50355/08_2025/9fff_50355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fff_50355/08_2025/9fff_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fff_50355/08_2025/9fff_50355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fff_50355/08_2025/9fff_50355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fff_50355/08_2025/9fff_50355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fff_50355/08_2025/9fff_50355.map" } resolution = 3.68 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'PHE:plan': 18, 'GLU:plan': 58, 'ARG:plan': 15, 'GLN:plan1': 39, 'ASN:plan1': 25, 'ASP:plan': 48, 'HIS:plan': 12, 'TYR:plan': 5, 'TRP:plan': 2} 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: {'GLU:plan': 34, 'GLN:plan1': 28, 'HIS:plan': 4, 'ASP:plan': 33, 'ARG:plan': 9, 'ASN:plan1': 13, 'TYR:plan': 1, 'PHE:plan': 2} 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: 2.69, per 1000 atoms: 0.18 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: 1.12 Conformation dependent library (CDL) restraints added in 674.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.86 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: 2.44 Time building geometry restraints manager: 1.55 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- 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= 0.138 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 : 11.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A1336 TYR 0.014 0.001 TYR A1297 PHE 0.028 0.001 PHE A1235 TRP 0.011 0.001 TRP A1165 HIS 0.005 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00282 (15441) covalent geometry : angle 0.64634 (21097) hydrogen bonds : bond 0.19203 ( 1113) hydrogen bonds : angle 6.20326 ( 3211) *********************** 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 to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.615 Fit side-chains REVERT: A 394 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6721 (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: 0.1060 time to fit residues: 18.0453 Evaluate side-chains 97 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 2.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 GLN A1325 GLN A1332 GLN A1339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.079686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.063202 restraints weight = 104590.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.063198 restraints weight = 67368.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.063776 restraints weight = 48157.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.063911 restraints weight = 38996.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.063967 restraints weight = 36285.091| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15441 Z= 0.250 Angle : 0.726 8.741 21097 Z= 0.380 Chirality : 0.043 0.214 2319 Planarity : 0.005 0.058 2556 Dihedral : 19.755 166.199 2864 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 6.81 % Allowed : 29.94 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 2025 helix: 1.12 (0.14), residues: 1477 sheet: None (None), residues: 0 loop : -1.93 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1336 TYR 0.018 0.002 TYR A1297 PHE 0.028 0.002 PHE A1067 TRP 0.013 0.002 TRP B1008 HIS 0.005 0.001 HIS B1269 Details of bonding type rmsd covalent geometry : bond 0.00543 (15441) covalent geometry : angle 0.72572 (21097) hydrogen bonds : bond 0.05489 ( 1113) hydrogen bonds : angle 4.77318 ( 3211) *********************** 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 175 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 94 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 LEU cc_start: 0.4812 (OUTLIER) cc_final: 0.4401 (mm) REVERT: B 705 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.9047 (m-10) outliers start: 81 outliers final: 50 residues processed: 163 average time/residue: 0.0940 time to fit residues: 25.6386 Evaluate side-chains 138 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 86 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 400 LYS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 664 PHE Chi-restraints excluded: chain A residue 732 LEU 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 1033 PHE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1140 ILE 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 346 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 427 ILE 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 769 ASN 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 884 LEU Chi-restraints excluded: chain B residue 921 MET 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 1088 LEU Chi-restraints excluded: chain B residue 1136 THR 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 1171 SER Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1175 HIS Chi-restraints excluded: chain B residue 1206 CYS Chi-restraints excluded: chain B residue 1260 ILE 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 179 optimal weight: 1.9990 chunk 16 optimal weight: 30.0000 chunk 207 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 191 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.081740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.064470 restraints weight = 102577.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.065755 restraints weight = 60868.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.066105 restraints weight = 40529.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.066501 restraints weight = 33258.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.066468 restraints weight = 28095.591| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1455 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= 0.137 Angle : 0.618 10.702 21097 Z= 0.314 Chirality : 0.040 0.302 2319 Planarity : 0.004 0.060 2556 Dihedral : 19.661 163.745 2862 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 4.63 % Allowed : 32.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.19), residues: 2025 helix: 1.41 (0.14), residues: 1482 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 358 TYR 0.018 0.001 TYR A1297 PHE 0.016 0.001 PHE A1367 TRP 0.015 0.001 TRP A1268 HIS 0.004 0.001 HIS B1175 Details of bonding type rmsd covalent geometry : bond 0.00296 (15441) covalent geometry : angle 0.61823 (21097) hydrogen bonds : bond 0.04756 ( 1113) hydrogen bonds : angle 4.26335 ( 3211) *********************** 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 154 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 99 time to evaluate : 0.750 Fit side-chains REVERT: A 736 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6101 (t80) REVERT: B 429 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8945 (pp) REVERT: B 462 ILE cc_start: 0.9101 (pt) cc_final: 0.8873 (mm) REVERT: B 705 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.9089 (m-10) REVERT: B 1170 THR cc_start: 0.7814 (p) cc_final: 0.7453 (t) outliers start: 55 outliers final: 27 residues processed: 147 average time/residue: 0.0927 time to fit residues: 23.2279 Evaluate side-chains 124 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 400 LYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 492 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 1064 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1145 MET 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 1312 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 769 ASN 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 1063 VAL Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1168 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 56 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 54 optimal weight: 0.0170 chunk 180 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 overall best weight: 4.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.078757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.061822 restraints weight = 103741.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.062365 restraints weight = 69698.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.062692 restraints weight = 45311.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.063016 restraints weight = 41542.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.063039 restraints weight = 37500.663| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15441 Z= 0.302 Angle : 0.776 10.102 21097 Z= 0.405 Chirality : 0.045 0.252 2319 Planarity : 0.005 0.053 2556 Dihedral : 19.884 163.938 2862 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 8.83 % Allowed : 28.76 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.19), residues: 2025 helix: 0.87 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 737 TYR 0.023 0.002 TYR A1297 PHE 0.023 0.003 PHE B1141 TRP 0.021 0.002 TRP A1148 HIS 0.006 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00650 (15441) covalent geometry : angle 0.77569 (21097) hydrogen bonds : bond 0.05649 ( 1113) hydrogen bonds : angle 4.90260 ( 3211) *********************** 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 195 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 90 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4644 (mm) REVERT: B 314 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (mp) REVERT: B 705 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.9046 (m-10) REVERT: B 716 MET cc_start: 0.9159 (mmp) cc_final: 0.8715 (mmm) REVERT: B 1275 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6163 (mtmm) outliers start: 105 outliers final: 67 residues processed: 184 average time/residue: 0.1004 time to fit residues: 30.4869 Evaluate side-chains 154 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 83 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 382 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 664 PHE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 923 TYR Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1064 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 1148 TRP Chi-restraints excluded: chain A residue 1150 ARG Chi-restraints excluded: chain A residue 1156 LEU 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 A residue 1316 SER Chi-restraints excluded: chain A residue 1340 HIS Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1357 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 769 ASN Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 857 GLU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 982 GLN Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1061 GLN Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1067 SER Chi-restraints excluded: chain B residue 1074 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1083 VAL Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1138 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 1209 PHE Chi-restraints excluded: chain B residue 1213 VAL Chi-restraints excluded: chain B residue 1260 ILE Chi-restraints excluded: chain B residue 1275 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 10 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.080109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.063150 restraints weight = 104149.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.063803 restraints weight = 69936.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.064050 restraints weight = 46155.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.064284 restraints weight = 41046.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.064376 restraints weight = 36778.675| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15441 Z= 0.187 Angle : 0.671 10.821 21097 Z= 0.344 Chirality : 0.041 0.276 2319 Planarity : 0.005 0.055 2556 Dihedral : 19.834 161.791 2856 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.49 % Allowed : 30.53 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.19), residues: 2025 helix: 1.07 (0.14), residues: 1465 sheet: None (None), residues: 0 loop : -1.82 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1370 TYR 0.020 0.002 TYR A1297 PHE 0.018 0.002 PHE A1367 TRP 0.018 0.002 TRP A1148 HIS 0.004 0.001 HIS B1175 Details of bonding type rmsd covalent geometry : bond 0.00413 (15441) covalent geometry : angle 0.67131 (21097) hydrogen bonds : bond 0.04899 ( 1113) hydrogen bonds : angle 4.55578 ( 3211) *********************** REFINEMENT MACRO_CYCLE 5 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 182 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 93 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4519 (mm) REVERT: B 429 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8941 (pp) REVERT: B 705 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9114 (m-10) REVERT: B 716 MET cc_start: 0.9213 (mmp) cc_final: 0.8781 (mmm) REVERT: B 1279 MET cc_start: 0.6946 (mmt) cc_final: 0.6689 (mmt) outliers start: 89 outliers final: 63 residues processed: 173 average time/residue: 0.0991 time to fit residues: 28.4353 Evaluate side-chains 151 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 85 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 382 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 664 PHE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 923 TYR Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1061 HIS Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1092 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 1148 TRP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1187 CYS 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 A residue 1316 SER Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1367 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 769 ASN 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 857 GLU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1061 GLN Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1067 SER 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 1098 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1153 SER Chi-restraints excluded: chain B residue 1168 ILE Chi-restraints excluded: chain B residue 1175 HIS Chi-restraints excluded: chain B residue 1209 PHE Chi-restraints excluded: chain B residue 1281 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1224 > 50: distance: 45 - 66: 4.512 distance: 49 - 72: 4.979 distance: 55 - 80: 3.562 distance: 59 - 66: 3.144 distance: 67 - 70: 4.759 distance: 70 - 71: 4.936 distance: 74 - 75: 3.875 distance: 80 - 81: 3.379 distance: 81 - 82: 3.004 distance: 81 - 84: 3.054 distance: 82 - 83: 3.672 distance: 82 - 90: 4.001 distance: 84 - 85: 4.994 distance: 85 - 86: 11.217 distance: 85 - 87: 6.352 distance: 86 - 88: 5.544 distance: 87 - 89: 9.537 distance: 88 - 89: 5.803 distance: 90 - 91: 7.292 distance: 91 - 92: 27.152 distance: 91 - 94: 6.977 distance: 92 - 93: 34.349 distance: 92 - 97: 11.358 distance: 94 - 95: 17.125 distance: 94 - 96: 18.580 distance: 97 - 98: 22.309 distance: 98 - 99: 22.383 distance: 98 - 101: 34.847 distance: 99 - 100: 46.552 distance: 99 - 105: 8.534 distance: 101 - 102: 42.679 distance: 102 - 103: 15.342 distance: 102 - 104: 22.927 distance: 105 - 106: 36.492 distance: 106 - 107: 30.288 distance: 106 - 109: 30.030 distance: 107 - 108: 33.280 distance: 107 - 117: 8.974 distance: 109 - 110: 27.130 distance: 110 - 111: 12.454 distance: 110 - 112: 4.169 distance: 111 - 113: 13.539 distance: 112 - 114: 23.932 distance: 113 - 115: 12.279 distance: 114 - 115: 13.766 distance: 115 - 116: 26.756 distance: 117 - 118: 16.067 distance: 118 - 119: 24.155 distance: 118 - 121: 12.820 distance: 119 - 120: 16.758 distance: 119 - 126: 13.372 distance: 121 - 122: 36.727 distance: 122 - 123: 19.844 distance: 123 - 124: 12.672 distance: 124 - 125: 6.261 distance: 126 - 127: 13.130 distance: 127 - 128: 17.698 distance: 127 - 130: 13.627 distance: 128 - 129: 19.190 distance: 128 - 132: 32.881 distance: 130 - 131: 35.556 distance: 132 - 133: 36.929 distance: 132 - 138: 30.999 distance: 133 - 134: 51.189 distance: 133 - 136: 23.275 distance: 134 - 135: 41.695 distance: 134 - 139: 37.549 distance: 135 - 160: 31.449 distance: 136 - 137: 37.911 distance: 137 - 138: 41.446 distance: 139 - 140: 35.762 distance: 140 - 141: 26.457 distance: 140 - 143: 19.257 distance: 141 - 142: 14.753 distance: 141 - 146: 27.137 distance: 142 - 167: 35.503 distance: 143 - 144: 31.568 distance: 143 - 145: 26.476