Starting phenix.real_space_refine on Thu Mar 5 14:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdy_13927/03_2026/7qdy_13927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdy_13927/03_2026/7qdy_13927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qdy_13927/03_2026/7qdy_13927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdy_13927/03_2026/7qdy_13927.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdy_13927/03_2026/7qdy_13927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdy_13927/03_2026/7qdy_13927.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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 6 5.49 5 S 107 5.16 5 C 14494 2.51 5 N 3981 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22924 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9065 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 75, 'TRANS': 1093} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 9007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9007 Classifications: {'peptide': 1212} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 26, 'TRANS': 1185} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'HIS:plan': 6, 'GLU:plan': 13, 'ASP:plan': 14, 'TYR:plan': 11, 'ARG:plan': 6, 'GLN:plan1': 4, 'ASN:plan1': 2, 'PHE:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 298 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 106 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.97, per 1000 atoms: 0.22 Number of scatterers: 22924 At special positions: 0 Unit cell: (180.454, 131.085, 142.15, 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 107 16.00 P 6 15.00 O 4336 8.00 N 3981 7.00 C 14494 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: 1.64 Conformation dependent library (CDL) restraints added in 985.2 milliseconds 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5606 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 22 sheets defined 51.9% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.744A pdb=" N SER A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.841A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.610A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.895A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 4.481A pdb=" N GLN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 3.664A pdb=" N LEU A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.689A pdb=" N ILE A 428 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.186A pdb=" N TRP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.931A pdb=" N TYR A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.870A pdb=" N GLY A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 3.799A pdb=" N ALA A 583 " --> pdb=" O CYS A 579 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.543A pdb=" N GLN A 617 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 631 removed outlier: 3.711A pdb=" N ARG A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.567A pdb=" N ILE A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 668 Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.579A pdb=" N TYR A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.649A pdb=" N ARG A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 761 through 768 removed outlier: 4.010A pdb=" N MET A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 778 through 794 removed outlier: 4.071A pdb=" N LYS A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 removed outlier: 3.700A pdb=" N LEU A 818 " --> pdb=" O TRP A 814 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.795A pdb=" N ASP A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 936 through 948 removed outlier: 4.452A pdb=" N LYS A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 Processing helix chain 'A' and resid 992 through 1010 removed outlier: 3.565A pdb=" N VAL A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1012 No H-bonds generated for 'chain 'A' and resid 1011 through 1012' Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1019 through 1044 removed outlier: 3.843A pdb=" N GLN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1075 through 1083 removed outlier: 3.715A pdb=" N ALA A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 3.851A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1128 through 1151 removed outlier: 3.999A pdb=" N GLU A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1181 through 1189 removed outlier: 3.808A pdb=" N LEU A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1205 removed outlier: 3.851A pdb=" N VAL A1197 " --> pdb=" O GLU A1193 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1205 " --> pdb=" O GLN A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1218 removed outlier: 3.625A pdb=" N GLY A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A1216 " --> pdb=" O GLY A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1230 removed outlier: 3.579A pdb=" N ALA A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.938A pdb=" N LYS B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.555A pdb=" N CYS B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.878A pdb=" N LEU B 460 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 461 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.526A pdb=" N GLY B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.607A pdb=" N LYS B 557 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 577 removed outlier: 3.812A pdb=" N ARG B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.592A pdb=" N TRP B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.663A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 4.017A pdb=" N VAL B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.787A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.820A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 3.731A pdb=" N ALA B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 726 removed outlier: 4.315A pdb=" N TRP B 717 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.677A pdb=" N LEU B 744 " --> pdb=" O GLY B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 removed outlier: 3.827A pdb=" N LEU B 772 " --> pdb=" O ARG B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 796 removed outlier: 3.516A pdb=" N TRP B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.592A pdb=" N TRP B 828 " --> pdb=" O ASN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 Processing helix chain 'B' and resid 860 through 874 removed outlier: 3.747A pdb=" N TRP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 908 removed outlier: 3.891A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 removed outlier: 3.505A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 976 Processing helix chain 'B' and resid 979 through 993 removed outlier: 4.047A pdb=" N PHE B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1010 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.505A pdb=" N THR B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1045 Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1080 removed outlier: 3.953A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1102 removed outlier: 3.825A pdb=" N GLN B1101 " --> pdb=" O THR B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1116 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'B' and resid 1137 through 1152 removed outlier: 4.528A pdb=" N SER B1141 " --> pdb=" O ASP B1137 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1172 removed outlier: 3.704A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.770A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1224 Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.177A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1313 removed outlier: 3.949A pdb=" N ASP B1313 " --> pdb=" O ALA B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 removed outlier: 3.646A pdb=" N ASN B1356 " --> pdb=" O ASN B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1371 Processing helix chain 'B' and resid 1382 through 1396 removed outlier: 3.708A pdb=" N ASN B1396 " --> pdb=" O THR B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.643A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1434 Processing helix chain 'B' and resid 1436 through 1456 removed outlier: 3.517A pdb=" N ALA B1456 " --> pdb=" O LYS B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1494 Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 3.799A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B1511 " --> pdb=" O ARG B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1533 Processing helix chain 'B' and resid 1535 through 1548 Processing helix chain 'B' and resid 1552 through 1563 removed outlier: 4.139A pdb=" N SER B1563 " --> pdb=" O GLN B1559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.760A pdb=" N ARG A 20 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 286 removed outlier: 6.709A pdb=" N ILE A 285 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER A 479 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 398 removed outlier: 7.181A pdb=" N ARG A 355 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ILE A 421 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 357 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU A 418 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE A 451 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 420 " --> pdb=" O ILE A 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507 removed outlier: 6.846A pdb=" N HIS A 489 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 676 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 570 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 569 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA A 661 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL A 571 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY A 633 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 683 removed outlier: 3.559A pdb=" N ARG A 690 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 916 through 920 removed outlier: 7.534A pdb=" N THR A 872 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 843 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS A 848 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 925 " --> pdb=" O LYS A 848 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 737 through 739 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 6.958A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 289 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 25 removed outlier: 6.242A pdb=" N LYS C 48 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 56 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.625A pdb=" N ALA C 79 " --> pdb=" O TRP C 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.714A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.600A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 196 through 198 removed outlier: 3.511A pdb=" N LEU C 205 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 215 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 235 through 240 removed outlier: 6.718A pdb=" N SER C 250 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 238 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 248 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE C 240 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N HIS C 246 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AB8, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.144A pdb=" N LYS D 48 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU D 56 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.697A pdb=" N LYS D 100 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AC2, first strand: chain 'D' and resid 154 through 156 removed outlier: 3.578A pdb=" N ALA D 164 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE D 172 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR D 185 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE D 174 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 196 through 197 removed outlier: 3.517A pdb=" N ILE D 214 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 216 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP D 218 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 224 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 235 through 239 removed outlier: 6.814A pdb=" N SER D 250 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL D 238 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 248 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 256 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) 1160 hydrogen bonds defined for protein. 3384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6344 1.33 - 1.45: 3983 1.45 - 1.57: 12878 1.57 - 1.69: 13 1.69 - 1.81: 168 Bond restraints: 23386 Sorted by residual: bond pdb=" CB VAL B 973 " pdb=" CG2 VAL B 973 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.48e+00 bond pdb=" CB ILE B 968 " pdb=" CG2 ILE B 968 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" CB ILE C 151 " pdb=" CG2 ILE C 151 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 bond pdb=" CG1 ILE B1182 " pdb=" CD1 ILE B1182 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.31e+00 bond pdb=" CB GLU C 141 " pdb=" CG GLU C 141 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.28e+00 ... (remaining 23381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 31163 3.41 - 6.82: 555 6.82 - 10.23: 47 10.23 - 13.64: 2 13.64 - 17.05: 4 Bond angle restraints: 31771 Sorted by residual: angle pdb=" N PRO B 417 " pdb=" CA PRO B 417 " pdb=" CB PRO B 417 " ideal model delta sigma weight residual 102.65 110.47 -7.82 6.80e-01 2.16e+00 1.32e+02 angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.25 111.52 -8.27 1.05e+00 9.07e-01 6.21e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" CB PRO A 206 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 angle pdb=" CA PRO B1294 " pdb=" N PRO B1294 " pdb=" CD PRO B1294 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.09e+01 angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" CB PRO B 386 " ideal model delta sigma weight residual 102.86 110.23 -7.37 1.23e+00 6.61e-01 3.59e+01 ... (remaining 31766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12614 17.94 - 35.87: 1236 35.87 - 53.80: 183 53.80 - 71.74: 45 71.74 - 89.67: 17 Dihedral angle restraints: 14095 sinusoidal: 5417 harmonic: 8678 Sorted by residual: dihedral pdb=" CA LEU A 586 " pdb=" C LEU A 586 " pdb=" N THR A 587 " pdb=" CA THR A 587 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N LYS C 140 " pdb=" CA LYS C 140 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 14092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2855 0.074 - 0.148: 715 0.148 - 0.222: 70 0.222 - 0.296: 5 0.296 - 0.370: 3 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CB ILE B 968 " pdb=" CA ILE B 968 " pdb=" CG1 ILE B 968 " pdb=" CG2 ILE B 968 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB VAL B 973 " pdb=" CA VAL B 973 " pdb=" CG1 VAL B 973 " pdb=" CG2 VAL B 973 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA MET A 671 " pdb=" N MET A 671 " pdb=" C MET A 671 " pdb=" CB MET A 671 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3645 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B1293 " 0.124 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO B1294 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO B1294 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO B1294 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 766 " 0.031 2.00e-02 2.50e+03 2.89e-02 1.67e+01 pdb=" CG TYR B 766 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR B 766 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 766 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 766 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 766 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 766 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 766 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 198 " -0.023 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE C 198 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE C 198 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 198 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE C 198 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 198 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 198 " 0.000 2.00e-02 2.50e+03 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 135 2.51 - 3.11: 17244 3.11 - 3.70: 33606 3.70 - 4.30: 46907 4.30 - 4.90: 80156 Nonbonded interactions: 178048 Sorted by model distance: nonbonded pdb=" OG SER C 251 " pdb=" OD1 ASP C 253 " model vdw 1.910 3.040 nonbonded pdb=" OH TYR A 358 " pdb=" OD2 ASP A 423 " model vdw 1.940 3.040 nonbonded pdb=" OE1 GLU A 663 " pdb=" O2' U E 2 " model vdw 2.034 3.040 nonbonded pdb=" NH1 ARG A 576 " pdb=" OP1 U E 2 " model vdw 2.054 3.120 nonbonded pdb=" OG SER C 209 " pdb=" OD1 ASP C 211 " model vdw 2.073 3.040 ... (remaining 178043 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.320 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.009 0.107 23386 Z= 0.390 Angle : 1.113 17.045 31771 Z= 0.605 Chirality : 0.062 0.370 3648 Planarity : 0.008 0.181 4076 Dihedral : 14.606 89.674 8489 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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 are not related in a simple way. whole: -1.41 (0.15), residues: 2975 helix: 0.96 (0.14), residues: 1458 sheet: -1.78 (0.26), residues: 340 loop : -3.25 (0.14), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG B 918 TYR 0.070 0.005 TYR B 766 PHE 0.064 0.005 PHE C 198 TRP 0.046 0.004 TRP D 24 HIS 0.027 0.003 HIS B1187 Details of bonding type rmsd covalent geometry : bond 0.00946 (23386) covalent geometry : angle 1.11312 (31771) hydrogen bonds : bond 0.16750 ( 1160) hydrogen bonds : angle 6.05656 ( 3384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.827 Fit side-chains REVERT: A 671 MET cc_start: 0.5952 (mpp) cc_final: 0.5540 (mpp) REVERT: B 518 ARG cc_start: 0.5583 (mtp-110) cc_final: 0.5256 (tpt90) REVERT: B 1146 ASN cc_start: 0.7827 (m110) cc_final: 0.7458 (m110) REVERT: C 53 ARG cc_start: 0.7973 (ptm-80) cc_final: 0.7632 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1590 time to fit residues: 47.8405 Evaluate side-chains 159 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 926 HIS B1011 GLN B1253 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132034 restraints weight = 34007.829| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.66 r_work: 0.3192 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23386 Z= 0.142 Angle : 0.673 12.383 31771 Z= 0.350 Chirality : 0.043 0.205 3648 Planarity : 0.005 0.094 4076 Dihedral : 6.594 76.596 3290 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.77 % Favored : 91.19 % Rotamer: Outliers : 0.63 % Allowed : 7.18 % Favored : 92.19 % 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 are not related in a simple way. whole: -0.80 (0.15), residues: 2975 helix: 1.38 (0.14), residues: 1462 sheet: -1.37 (0.28), residues: 326 loop : -2.88 (0.15), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 576 TYR 0.017 0.002 TYR B 935 PHE 0.022 0.002 PHE D 247 TRP 0.029 0.001 TRP D 47 HIS 0.008 0.001 HIS B1187 Details of bonding type rmsd covalent geometry : bond 0.00304 (23386) covalent geometry : angle 0.67293 (31771) hydrogen bonds : bond 0.05006 ( 1160) hydrogen bonds : angle 4.58809 ( 3384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.770 Fit side-chains REVERT: A 671 MET cc_start: 0.6380 (mpp) cc_final: 0.5959 (mpp) REVERT: A 1031 MET cc_start: 0.3933 (ppp) cc_final: 0.3305 (ttp) REVERT: B 518 ARG cc_start: 0.6170 (mtp-110) cc_final: 0.5143 (tpt90) REVERT: B 544 MET cc_start: 0.6683 (ptm) cc_final: 0.6471 (tmm) REVERT: B 576 LYS cc_start: 0.6622 (mtpp) cc_final: 0.6377 (mttm) REVERT: B 1146 ASN cc_start: 0.7876 (m110) cc_final: 0.7387 (m110) REVERT: B 1338 ASP cc_start: 0.7317 (t0) cc_final: 0.6908 (m-30) REVERT: C 53 ARG cc_start: 0.7880 (ptm-80) cc_final: 0.7518 (ptm-80) outliers start: 15 outliers final: 10 residues processed: 207 average time/residue: 0.1594 time to fit residues: 52.4367 Evaluate side-chains 185 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 20 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS A1032 GLN B 580 HIS B1253 ASN B1356 ASN ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1529 HIS ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.164888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124485 restraints weight = 34148.806| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.75 r_work: 0.3228 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23386 Z= 0.243 Angle : 0.747 13.414 31771 Z= 0.389 Chirality : 0.048 0.266 3648 Planarity : 0.006 0.073 4076 Dihedral : 6.702 74.891 3290 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 1.69 % Allowed : 10.64 % Favored : 87.67 % 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 are not related in a simple way. whole: -0.95 (0.15), residues: 2975 helix: 1.13 (0.14), residues: 1460 sheet: -1.21 (0.28), residues: 342 loop : -2.85 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1201 TYR 0.024 0.003 TYR B1320 PHE 0.024 0.002 PHE C 240 TRP 0.022 0.002 TRP D 47 HIS 0.010 0.002 HIS B1187 Details of bonding type rmsd covalent geometry : bond 0.00589 (23386) covalent geometry : angle 0.74653 (31771) hydrogen bonds : bond 0.06524 ( 1160) hydrogen bonds : angle 4.47151 ( 3384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.6385 (mpp) cc_final: 0.6027 (mpp) REVERT: A 778 ASP cc_start: 0.8094 (p0) cc_final: 0.7527 (p0) REVERT: B 518 ARG cc_start: 0.6058 (mtp-110) cc_final: 0.5071 (tpt90) REVERT: B 576 LYS cc_start: 0.6660 (mtpp) cc_final: 0.6418 (mttm) REVERT: C 53 ARG cc_start: 0.7894 (ptm-80) cc_final: 0.7545 (ptm-80) REVERT: C 184 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.7253 (p90) REVERT: C 210 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: D 156 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.6236 (t80) outliers start: 40 outliers final: 25 residues processed: 212 average time/residue: 0.1481 time to fit residues: 50.6642 Evaluate side-chains 203 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1253 ASN Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 144 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 270 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS B 580 HIS B 879 GLN B1356 ASN ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1491 GLN D 126 HIS ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116345 restraints weight = 33801.897| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.30 r_work: 0.3172 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23386 Z= 0.210 Angle : 0.698 12.756 31771 Z= 0.366 Chirality : 0.046 0.248 3648 Planarity : 0.005 0.070 4076 Dihedral : 6.654 74.811 3290 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.01 % Favored : 90.96 % Rotamer: Outliers : 2.70 % Allowed : 12.16 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 2975 helix: 1.06 (0.14), residues: 1472 sheet: -1.07 (0.28), residues: 346 loop : -2.83 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1201 TYR 0.021 0.002 TYR A 697 PHE 0.018 0.002 PHE B1112 TRP 0.021 0.002 TRP D 47 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd covalent geometry : bond 0.00505 (23386) covalent geometry : angle 0.69778 (31771) hydrogen bonds : bond 0.05910 ( 1160) hydrogen bonds : angle 4.30400 ( 3384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 778 ASP cc_start: 0.8102 (p0) cc_final: 0.7579 (p0) REVERT: B 518 ARG cc_start: 0.6035 (mtp-110) cc_final: 0.5053 (tpt90) REVERT: B 544 MET cc_start: 0.6784 (ptm) cc_final: 0.6500 (tmm) REVERT: B 795 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 1475 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 1496 MET cc_start: 0.6889 (tmm) cc_final: 0.6656 (tmm) REVERT: B 1528 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.6020 (ttp-170) REVERT: C 53 ARG cc_start: 0.7869 (ptm-80) cc_final: 0.7525 (ptm-80) REVERT: C 151 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 184 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7372 (p90) REVERT: C 210 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8653 (m-30) REVERT: D 50 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6681 (mmp80) REVERT: D 132 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7389 (mp) REVERT: D 156 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.6650 (t80) outliers start: 64 outliers final: 37 residues processed: 237 average time/residue: 0.1573 time to fit residues: 59.3036 Evaluate side-chains 216 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1286 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain B residue 1528 ARG Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 44 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 278 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 193 optimal weight: 0.6980 chunk 257 optimal weight: 0.9980 chunk 78 optimal weight: 0.0030 chunk 68 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 148 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS B 580 HIS B 874 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1411 GLN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1432 GLN D 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129599 restraints weight = 33451.891| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 4.79 r_work: 0.3166 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23386 Z= 0.132 Angle : 0.601 12.212 31771 Z= 0.316 Chirality : 0.042 0.204 3648 Planarity : 0.004 0.067 4076 Dihedral : 6.362 75.788 3290 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.50 % Rotamer: Outliers : 2.36 % Allowed : 13.59 % Favored : 84.04 % 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 are not related in a simple way. whole: -0.60 (0.15), residues: 2975 helix: 1.42 (0.14), residues: 1470 sheet: -0.89 (0.28), residues: 337 loop : -2.76 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 630 TYR 0.017 0.001 TYR B 954 PHE 0.014 0.001 PHE D 150 TRP 0.018 0.001 TRP D 47 HIS 0.005 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00294 (23386) covalent geometry : angle 0.60135 (31771) hydrogen bonds : bond 0.04476 ( 1160) hydrogen bonds : angle 4.02203 ( 3384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7343 (OUTLIER) cc_final: 0.5763 (m-90) REVERT: A 778 ASP cc_start: 0.7947 (p0) cc_final: 0.7582 (p0) REVERT: A 1031 MET cc_start: 0.5281 (mmt) cc_final: 0.5068 (ttt) REVERT: B 518 ARG cc_start: 0.6184 (mtp-110) cc_final: 0.5160 (tpt90) REVERT: B 544 MET cc_start: 0.6815 (ptm) cc_final: 0.6595 (tmm) REVERT: B 795 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 1400 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7752 (t) REVERT: B 1496 MET cc_start: 0.6896 (tmm) cc_final: 0.6645 (tmm) REVERT: B 1528 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.6056 (ttp-170) REVERT: C 53 ARG cc_start: 0.7806 (ptm-80) cc_final: 0.7442 (ptm-80) REVERT: C 141 GLU cc_start: 0.6743 (mp0) cc_final: 0.6512 (mp0) REVERT: C 184 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.7283 (p90) REVERT: C 210 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: D 132 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7159 (mp) REVERT: D 156 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6372 (t80) outliers start: 56 outliers final: 26 residues processed: 234 average time/residue: 0.1520 time to fit residues: 57.5501 Evaluate side-chains 205 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1286 LEU Chi-restraints excluded: chain B residue 1356 ASN Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain B residue 1528 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 246 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 34 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 253 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 148 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS B1356 ASN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130709 restraints weight = 33524.099| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.37 r_work: 0.3101 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23386 Z= 0.154 Angle : 0.623 12.622 31771 Z= 0.325 Chirality : 0.043 0.212 3648 Planarity : 0.004 0.064 4076 Dihedral : 6.317 75.462 3290 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.91 % Favored : 91.06 % Rotamer: Outliers : 2.53 % Allowed : 14.90 % Favored : 82.57 % 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 are not related in a simple way. whole: -0.53 (0.16), residues: 2975 helix: 1.45 (0.14), residues: 1475 sheet: -0.80 (0.28), residues: 342 loop : -2.73 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 630 TYR 0.016 0.002 TYR B 954 PHE 0.015 0.002 PHE B1112 TRP 0.015 0.001 TRP D 47 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00359 (23386) covalent geometry : angle 0.62299 (31771) hydrogen bonds : bond 0.04881 ( 1160) hydrogen bonds : angle 3.99424 ( 3384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7312 (OUTLIER) cc_final: 0.5742 (m-90) REVERT: A 778 ASP cc_start: 0.8034 (p0) cc_final: 0.7649 (p0) REVERT: A 1031 MET cc_start: 0.5487 (mmt) cc_final: 0.5085 (ttm) REVERT: B 518 ARG cc_start: 0.6073 (mtp-110) cc_final: 0.5070 (tpt90) REVERT: B 770 LEU cc_start: 0.8408 (tp) cc_final: 0.8068 (mt) REVERT: B 795 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 1035 GLU cc_start: 0.8296 (mp0) cc_final: 0.7970 (mp0) REVERT: B 1475 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7192 (mm) REVERT: B 1496 MET cc_start: 0.6944 (tmm) cc_final: 0.6706 (tmm) REVERT: B 1528 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6446 (ttp-170) REVERT: C 53 ARG cc_start: 0.7870 (ptm-80) cc_final: 0.7538 (ptm-80) REVERT: C 141 GLU cc_start: 0.6983 (mp0) cc_final: 0.6700 (mp0) REVERT: C 184 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.7420 (p90) REVERT: C 210 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (m-30) REVERT: D 132 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7290 (mp) REVERT: D 156 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.6502 (t80) outliers start: 60 outliers final: 37 residues processed: 227 average time/residue: 0.1555 time to fit residues: 56.3799 Evaluate side-chains 218 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1286 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain B residue 1528 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 268 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 223 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 177 optimal weight: 0.2980 chunk 137 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 HIS A 390 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.167928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119303 restraints weight = 33744.769| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.25 r_work: 0.3203 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23386 Z= 0.120 Angle : 0.581 11.871 31771 Z= 0.303 Chirality : 0.041 0.186 3648 Planarity : 0.004 0.059 4076 Dihedral : 6.147 75.675 3290 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.57 % Favored : 91.39 % Rotamer: Outliers : 2.49 % Allowed : 15.32 % Favored : 82.19 % 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 are not related in a simple way. whole: -0.28 (0.16), residues: 2975 helix: 1.67 (0.14), residues: 1475 sheet: -0.60 (0.29), residues: 333 loop : -2.67 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 53 TYR 0.025 0.001 TYR A 697 PHE 0.013 0.001 PHE D 150 TRP 0.016 0.001 TRP D 47 HIS 0.007 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00264 (23386) covalent geometry : angle 0.58078 (31771) hydrogen bonds : bond 0.04023 ( 1160) hydrogen bonds : angle 3.81697 ( 3384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7273 (OUTLIER) cc_final: 0.5696 (m-90) REVERT: A 639 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7313 (pt) REVERT: A 663 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 778 ASP cc_start: 0.7966 (p0) cc_final: 0.7687 (p0) REVERT: A 793 LEU cc_start: 0.2659 (OUTLIER) cc_final: 0.2336 (tt) REVERT: A 1031 MET cc_start: 0.5449 (mmt) cc_final: 0.5088 (ttt) REVERT: B 518 ARG cc_start: 0.6117 (mtp-110) cc_final: 0.5070 (tpt90) REVERT: B 770 LEU cc_start: 0.8332 (tp) cc_final: 0.7993 (mt) REVERT: B 795 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 1035 GLU cc_start: 0.8356 (mp0) cc_final: 0.8023 (mp0) REVERT: B 1341 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5967 (mtm180) REVERT: B 1400 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7805 (t) REVERT: B 1475 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6759 (mt) REVERT: B 1496 MET cc_start: 0.6960 (tmm) cc_final: 0.6691 (tmm) REVERT: C 53 ARG cc_start: 0.7768 (ptm-80) cc_final: 0.7437 (ptm-80) REVERT: C 141 GLU cc_start: 0.6921 (mp0) cc_final: 0.6562 (mp0) REVERT: C 184 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.7175 (p90) REVERT: C 210 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8542 (m-30) REVERT: C 285 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8254 (p0) REVERT: D 132 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7180 (mp) REVERT: D 156 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.6270 (t80) outliers start: 59 outliers final: 30 residues processed: 238 average time/residue: 0.1436 time to fit residues: 54.8863 Evaluate side-chains 221 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1341 ARG Chi-restraints excluded: chain B residue 1356 ASN Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 279 optimal weight: 0.8980 chunk 232 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 219 optimal weight: 0.3980 chunk 275 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS B 580 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126963 restraints weight = 33610.874| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.76 r_work: 0.3275 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23386 Z= 0.129 Angle : 0.594 12.615 31771 Z= 0.308 Chirality : 0.042 0.206 3648 Planarity : 0.004 0.057 4076 Dihedral : 6.100 75.521 3290 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.44 % Favored : 91.53 % Rotamer: Outliers : 2.15 % Allowed : 15.70 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2975 helix: 1.71 (0.14), residues: 1478 sheet: -0.50 (0.29), residues: 332 loop : -2.65 (0.16), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 53 TYR 0.035 0.001 TYR B 517 PHE 0.015 0.001 PHE B1112 TRP 0.014 0.001 TRP D 47 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00288 (23386) covalent geometry : angle 0.59362 (31771) hydrogen bonds : bond 0.04231 ( 1160) hydrogen bonds : angle 3.79439 ( 3384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7239 (OUTLIER) cc_final: 0.5735 (m-90) REVERT: A 639 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7266 (pt) REVERT: A 726 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5800 (ptt) REVERT: A 778 ASP cc_start: 0.8020 (p0) cc_final: 0.7743 (p0) REVERT: A 793 LEU cc_start: 0.2557 (OUTLIER) cc_final: 0.2226 (tt) REVERT: A 1098 ASN cc_start: 0.6688 (t0) cc_final: 0.6185 (t0) REVERT: B 518 ARG cc_start: 0.6162 (mtp-110) cc_final: 0.5072 (tpt90) REVERT: B 657 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8035 (ptp) REVERT: B 770 LEU cc_start: 0.8301 (tp) cc_final: 0.7971 (mt) REVERT: B 795 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 1035 GLU cc_start: 0.8248 (mp0) cc_final: 0.8002 (mp0) REVERT: B 1341 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6033 (mtm180) REVERT: B 1400 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7867 (t) REVERT: B 1475 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7127 (mm) REVERT: B 1496 MET cc_start: 0.6959 (tmm) cc_final: 0.6693 (tmm) REVERT: C 53 ARG cc_start: 0.7766 (ptm-80) cc_final: 0.7437 (ptm-80) REVERT: C 184 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.7286 (p90) REVERT: C 187 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: C 210 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: D 132 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7130 (mp) REVERT: D 156 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.6240 (t80) outliers start: 51 outliers final: 32 residues processed: 220 average time/residue: 0.1521 time to fit residues: 53.1622 Evaluate side-chains 224 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 179 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1293 GLN Chi-restraints excluded: chain B residue 1341 ARG Chi-restraints excluded: chain B residue 1356 ASN Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 183 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS B1356 ASN B1432 GLN C 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117777 restraints weight = 33725.652| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.20 r_work: 0.3185 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23386 Z= 0.143 Angle : 0.612 12.846 31771 Z= 0.319 Chirality : 0.042 0.205 3648 Planarity : 0.004 0.054 4076 Dihedral : 6.138 74.825 3290 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.97 % Favored : 90.99 % Rotamer: Outliers : 2.28 % Allowed : 15.70 % Favored : 82.02 % 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 are not related in a simple way. whole: -0.23 (0.16), residues: 2975 helix: 1.69 (0.14), residues: 1479 sheet: -0.39 (0.29), residues: 330 loop : -2.66 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 53 TYR 0.028 0.001 TYR B 517 PHE 0.012 0.001 PHE B1112 TRP 0.013 0.001 TRP D 47 HIS 0.007 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00327 (23386) covalent geometry : angle 0.61228 (31771) hydrogen bonds : bond 0.04522 ( 1160) hydrogen bonds : angle 3.82166 ( 3384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7387 (ptp90) REVERT: A 307 TRP cc_start: 0.7265 (OUTLIER) cc_final: 0.5702 (m-90) REVERT: A 639 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7337 (pt) REVERT: A 726 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5936 (ptt) REVERT: A 778 ASP cc_start: 0.8060 (p0) cc_final: 0.7804 (p0) REVERT: A 793 LEU cc_start: 0.2575 (OUTLIER) cc_final: 0.2256 (tt) REVERT: B 518 ARG cc_start: 0.6137 (mtp-110) cc_final: 0.5057 (tpt90) REVERT: B 657 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8126 (ptp) REVERT: B 770 LEU cc_start: 0.8372 (tp) cc_final: 0.8034 (mt) REVERT: B 795 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8210 (tm-30) REVERT: B 1035 GLU cc_start: 0.8347 (mp0) cc_final: 0.8036 (mp0) REVERT: B 1341 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6125 (mtm180) REVERT: B 1400 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7889 (t) REVERT: B 1475 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7104 (mm) REVERT: C 53 ARG cc_start: 0.7797 (ptm-80) cc_final: 0.7475 (ptm-80) REVERT: C 141 GLU cc_start: 0.6972 (mp0) cc_final: 0.6675 (mp0) REVERT: C 184 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.7281 (p90) REVERT: C 187 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: C 210 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8579 (m-30) REVERT: C 285 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8239 (p0) REVERT: D 132 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7127 (mp) REVERT: D 156 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.6431 (t80) outliers start: 54 outliers final: 36 residues processed: 215 average time/residue: 0.1600 time to fit residues: 54.9848 Evaluate side-chains 226 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1293 GLN Chi-restraints excluded: chain B residue 1341 ARG Chi-restraints excluded: chain B residue 1356 ASN Chi-restraints excluded: chain B residue 1374 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 114 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS B1356 ASN C 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.166455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117246 restraints weight = 33806.647| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.30 r_work: 0.3179 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 23386 Z= 0.159 Angle : 0.760 59.191 31771 Z= 0.422 Chirality : 0.043 0.403 3648 Planarity : 0.005 0.135 4076 Dihedral : 6.189 74.811 3290 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.94 % Favored : 91.03 % Rotamer: Outliers : 2.11 % Allowed : 15.96 % Favored : 81.93 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.23 (0.16), residues: 2975 helix: 1.68 (0.14), residues: 1479 sheet: -0.39 (0.29), residues: 330 loop : -2.66 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 630 TYR 0.025 0.001 TYR B 517 PHE 0.011 0.001 PHE D 150 TRP 0.013 0.001 TRP D 47 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00342 (23386) covalent geometry : angle 0.75957 (31771) hydrogen bonds : bond 0.04512 ( 1160) hydrogen bonds : angle 3.82121 ( 3384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7390 (ptp90) REVERT: A 307 TRP cc_start: 0.7261 (OUTLIER) cc_final: 0.5680 (m-90) REVERT: A 639 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7356 (pt) REVERT: A 726 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5945 (ptt) REVERT: A 778 ASP cc_start: 0.8056 (p0) cc_final: 0.7790 (p0) REVERT: A 793 LEU cc_start: 0.2563 (OUTLIER) cc_final: 0.2247 (tt) REVERT: B 518 ARG cc_start: 0.6149 (mtp-110) cc_final: 0.5051 (tpt90) REVERT: B 657 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8136 (ptp) REVERT: B 770 LEU cc_start: 0.8374 (tp) cc_final: 0.8034 (mt) REVERT: B 795 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8207 (tm-30) REVERT: B 1035 GLU cc_start: 0.8378 (mp0) cc_final: 0.8060 (mp0) REVERT: B 1341 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6151 (mtm180) REVERT: B 1356 ASN cc_start: 0.5069 (OUTLIER) cc_final: 0.4505 (m-40) REVERT: B 1400 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7899 (t) REVERT: B 1475 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7098 (mm) REVERT: C 53 ARG cc_start: 0.7799 (ptm-80) cc_final: 0.7479 (ptm-80) REVERT: C 141 GLU cc_start: 0.6999 (mp0) cc_final: 0.6696 (mp0) REVERT: C 184 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7287 (p90) REVERT: C 187 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6526 (tt0) REVERT: C 210 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8598 (m-30) REVERT: D 132 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7131 (mp) REVERT: D 156 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6439 (t80) outliers start: 50 outliers final: 33 residues processed: 211 average time/residue: 0.1676 time to fit residues: 56.4821 Evaluate side-chains 221 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1293 GLN Chi-restraints excluded: chain B residue 1341 ARG Chi-restraints excluded: chain B residue 1356 ASN Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1422 CYS Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1486 LEU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 51 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 1 optimal weight: 0.1980 chunk 170 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.166431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116742 restraints weight = 33607.333| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.17 r_work: 0.3174 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 23386 Z= 0.159 Angle : 0.760 59.191 31771 Z= 0.422 Chirality : 0.043 0.403 3648 Planarity : 0.005 0.135 4076 Dihedral : 6.189 74.811 3290 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.94 % Favored : 91.03 % Rotamer: Outliers : 2.03 % Allowed : 16.00 % Favored : 81.98 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.23 (0.16), residues: 2975 helix: 1.68 (0.14), residues: 1479 sheet: -0.39 (0.29), residues: 330 loop : -2.66 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 630 TYR 0.025 0.001 TYR B 517 PHE 0.011 0.001 PHE D 150 TRP 0.013 0.001 TRP D 47 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00342 (23386) covalent geometry : angle 0.75957 (31771) hydrogen bonds : bond 0.04512 ( 1160) hydrogen bonds : angle 3.82121 ( 3384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6823.73 seconds wall clock time: 117 minutes 12.70 seconds (7032.70 seconds total)