Starting phenix.real_space_refine on Thu Jun 19 21:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdy_13927/06_2025/7qdy_13927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdy_13927/06_2025/7qdy_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_13927/06_2025/7qdy_13927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdy_13927/06_2025/7qdy_13927.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdy_13927/06_2025/7qdy_13927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdy_13927/06_2025/7qdy_13927.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 4, 'HIS:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 6} 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: 14.24, per 1000 atoms: 0.62 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: 5.64 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.72 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: 9.31 Time building geometry restraints manager: 6.69 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: 8.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 53.510 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.690 ------------------------------------------------------------------------------- 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 : 11.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (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 TRP 0.046 0.004 TRP D 24 HIS 0.027 0.003 HIS B1187 PHE 0.064 0.005 PHE C 198 TYR 0.070 0.005 TYR B 766 ARG 0.022 0.002 ARG B 918 Details of bonding type rmsd hydrogen bonds : bond 0.16750 ( 1160) hydrogen bonds : angle 6.05656 ( 3384) covalent geometry : bond 0.00946 (23386) covalent geometry : angle 1.11312 (31771) *********************** 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 : 2.348 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: 0.3794 time to fit residues: 113.3068 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 : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 225 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 141 optimal weight: 0.5980 chunk 173 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 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 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS 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** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.167101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132908 restraints weight = 33717.530| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.27 r_work: 0.3163 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23386 Z= 0.167 Angle : 0.705 13.051 31771 Z= 0.367 Chirality : 0.045 0.228 3648 Planarity : 0.005 0.095 4076 Dihedral : 6.683 75.548 3290 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.94 % Favored : 91.03 % Rotamer: Outliers : 0.68 % Allowed : 7.77 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 2975 helix: 1.27 (0.14), residues: 1462 sheet: -1.37 (0.28), residues: 328 loop : -2.88 (0.15), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 47 HIS 0.008 0.001 HIS B1187 PHE 0.023 0.002 PHE D 247 TYR 0.019 0.002 TYR B1320 ARG 0.012 0.001 ARG B1528 Details of bonding type rmsd hydrogen bonds : bond 0.05657 ( 1160) hydrogen bonds : angle 4.64501 ( 3384) covalent geometry : bond 0.00376 (23386) covalent geometry : angle 0.70532 (31771) *********************** 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 209 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 2.373 Fit side-chains REVERT: A 671 MET cc_start: 0.6325 (mpp) cc_final: 0.6002 (mpp) REVERT: A 778 ASP cc_start: 0.8094 (p0) cc_final: 0.7654 (p0) REVERT: A 1031 MET cc_start: 0.3828 (ppp) cc_final: 0.3196 (ttp) REVERT: A 1126 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 518 ARG cc_start: 0.6184 (mtp-110) cc_final: 0.5174 (tpt90) REVERT: B 576 LYS cc_start: 0.6621 (mtpp) cc_final: 0.6354 (mttm) REVERT: B 770 LEU cc_start: 0.8364 (tp) cc_final: 0.8161 (tp) REVERT: B 1146 ASN cc_start: 0.7941 (m110) cc_final: 0.7456 (m110) REVERT: B 1338 ASP cc_start: 0.7348 (t0) cc_final: 0.7007 (m-30) REVERT: B 1359 GLN cc_start: 0.7251 (pm20) cc_final: 0.6903 (pm20) REVERT: C 53 ARG cc_start: 0.7933 (ptm-80) cc_final: 0.7567 (ptm-80) outliers start: 16 outliers final: 11 residues processed: 200 average time/residue: 0.3361 time to fit residues: 106.1352 Evaluate side-chains 188 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 973 VAL 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 C residue 168 ILE 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 202 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A1032 GLN B 580 HIS B1253 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** 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 = 0.4064 r_free = 0.4064 target = 0.166322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132551 restraints weight = 33778.685| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.46 r_work: 0.3151 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23386 Z= 0.145 Angle : 0.634 11.836 31771 Z= 0.331 Chirality : 0.043 0.207 3648 Planarity : 0.005 0.069 4076 Dihedral : 6.443 76.267 3290 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.10 % Favored : 91.87 % Rotamer: Outliers : 1.73 % Allowed : 9.92 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2975 helix: 1.42 (0.14), residues: 1461 sheet: -1.08 (0.28), residues: 329 loop : -2.80 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 47 HIS 0.005 0.001 HIS C 126 PHE 0.016 0.002 PHE D 150 TYR 0.016 0.002 TYR B1320 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 1160) hydrogen bonds : angle 4.23571 ( 3384) covalent geometry : bond 0.00326 (23386) covalent geometry : angle 0.63431 (31771) *********************** 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 238 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 2.403 Fit side-chains revert: symmetry clash REVERT: A 671 MET cc_start: 0.6468 (mpp) cc_final: 0.6074 (mpp) REVERT: A 778 ASP cc_start: 0.7875 (p0) cc_final: 0.7506 (p0) REVERT: A 1031 MET cc_start: 0.3977 (ppp) cc_final: 0.3432 (ttm) REVERT: B 518 ARG cc_start: 0.6105 (mtp-110) cc_final: 0.5103 (tpt90) REVERT: C 53 ARG cc_start: 0.7886 (ptm-80) cc_final: 0.7534 (ptm-80) REVERT: C 184 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7086 (p90) REVERT: C 210 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8469 (m-30) REVERT: D 156 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6177 (t80) outliers start: 41 outliers final: 25 residues processed: 225 average time/residue: 0.3464 time to fit residues: 123.1249 Evaluate side-chains 207 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 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 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 218 ASP 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 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 42 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 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 B 580 HIS B 879 GLN B1356 ASN B1396 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** B1491 GLN B1529 HIS C 285 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.163843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115145 restraints weight = 33933.100| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.25 r_work: 0.3136 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1768 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= 0.237 Angle : 0.728 13.103 31771 Z= 0.380 Chirality : 0.047 0.251 3648 Planarity : 0.005 0.069 4076 Dihedral : 6.623 75.055 3290 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.18 % Favored : 90.79 % Rotamer: Outliers : 2.49 % Allowed : 11.99 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 2975 helix: 1.13 (0.14), residues: 1469 sheet: -1.04 (0.28), residues: 340 loop : -2.81 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 47 HIS 0.008 0.002 HIS A 623 PHE 0.018 0.002 PHE C 240 TYR 0.020 0.002 TYR A 697 ARG 0.006 0.001 ARG B1201 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 1160) hydrogen bonds : angle 4.31652 ( 3384) covalent geometry : bond 0.00576 (23386) covalent geometry : angle 0.72785 (31771) *********************** 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 240 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 2.314 Fit side-chains revert: symmetry clash REVERT: A 778 ASP cc_start: 0.8027 (p0) cc_final: 0.7563 (p0) REVERT: B 518 ARG cc_start: 0.5936 (mtp-110) cc_final: 0.4993 (tpt90) REVERT: B 1496 MET cc_start: 0.6851 (tmm) cc_final: 0.6365 (tmm) REVERT: B 1528 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.6013 (ttp-170) REVERT: C 53 ARG cc_start: 0.7882 (ptm-80) cc_final: 0.7524 (ptm-80) REVERT: C 184 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.7335 (p90) REVERT: C 210 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8689 (m-30) REVERT: D 132 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7387 (mp) REVERT: D 156 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.6689 (t80) REVERT: D 161 LYS cc_start: 0.7326 (mmmm) cc_final: 0.7066 (mmmt) outliers start: 59 outliers final: 36 residues processed: 227 average time/residue: 0.3349 time to fit residues: 121.8693 Evaluate side-chains 215 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 175 GLU 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 700 MET Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain B residue 599 ASN 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 1486 LEU Chi-restraints excluded: chain B residue 1528 ARG Chi-restraints excluded: chain C residue 8 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 218 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 157 optimal weight: 0.9990 chunk 192 optimal weight: 0.0010 chunk 206 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 285 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 243 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 874 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1396 ASN B1411 GLN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN D 119 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.164965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116185 restraints weight = 33806.292| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.45 r_work: 0.3179 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23386 Z= 0.138 Angle : 0.612 11.324 31771 Z= 0.322 Chirality : 0.042 0.202 3648 Planarity : 0.004 0.067 4076 Dihedral : 6.384 76.610 3290 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.67 % Favored : 91.29 % Rotamer: Outliers : 2.53 % Allowed : 13.30 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 2975 helix: 1.42 (0.14), residues: 1471 sheet: -0.82 (0.28), residues: 333 loop : -2.76 (0.16), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 47 HIS 0.004 0.001 HIS A 623 PHE 0.016 0.001 PHE D 150 TYR 0.017 0.001 TYR B 954 ARG 0.004 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 1160) hydrogen bonds : angle 4.03899 ( 3384) covalent geometry : bond 0.00312 (23386) covalent geometry : angle 0.61244 (31771) *********************** 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 255 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 2.621 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7375 (OUTLIER) cc_final: 0.5769 (m-90) REVERT: A 778 ASP cc_start: 0.7894 (p0) cc_final: 0.7561 (p0) REVERT: A 830 MET cc_start: 0.2298 (mmm) cc_final: 0.1343 (mpp) REVERT: A 1031 MET cc_start: 0.3216 (ppp) cc_final: 0.2875 (ttm) REVERT: A 1067 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8657 (m-10) REVERT: B 518 ARG cc_start: 0.6111 (mtp-110) cc_final: 0.5104 (tpt90) REVERT: B 795 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 1400 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7857 (t) REVERT: B 1475 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7112 (mm) REVERT: B 1496 MET cc_start: 0.6969 (tmm) cc_final: 0.6758 (tmm) REVERT: B 1528 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.6043 (ttp-170) REVERT: C 53 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.7478 (ptm-80) REVERT: C 141 GLU cc_start: 0.6915 (mp0) cc_final: 0.6712 (mp0) REVERT: C 184 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7240 (p90) REVERT: C 210 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8581 (m-30) REVERT: C 285 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8433 (p0) REVERT: D 156 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6554 (t80) REVERT: D 161 LYS cc_start: 0.7387 (mmmm) cc_final: 0.7140 (mmmt) outliers start: 60 outliers final: 31 residues processed: 240 average time/residue: 0.3946 time to fit residues: 153.4397 Evaluate side-chains 216 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET 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 591 LEU Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 1067 TYR 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 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 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 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 285 ASN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 126 HIS 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 160 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 274 optimal weight: 0.6980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 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** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.167213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118645 restraints weight = 33790.106| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.18 r_work: 0.3185 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23386 Z= 0.141 Angle : 0.612 12.288 31771 Z= 0.319 Chirality : 0.042 0.201 3648 Planarity : 0.004 0.065 4076 Dihedral : 6.288 76.925 3290 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 2.32 % Allowed : 14.48 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2975 helix: 1.52 (0.14), residues: 1475 sheet: -0.77 (0.28), residues: 336 loop : -2.71 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 47 HIS 0.004 0.001 HIS D 15 PHE 0.018 0.001 PHE B1112 TYR 0.017 0.001 TYR B 954 ARG 0.004 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 1160) hydrogen bonds : angle 3.95974 ( 3384) covalent geometry : bond 0.00322 (23386) covalent geometry : angle 0.61161 (31771) *********************** 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 241 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 2.401 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7325 (OUTLIER) cc_final: 0.5742 (m-90) REVERT: A 778 ASP cc_start: 0.7883 (p0) cc_final: 0.7630 (p0) REVERT: A 1031 MET cc_start: 0.3604 (ppp) cc_final: 0.3031 (ttp) REVERT: A 1067 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8650 (m-10) REVERT: B 518 ARG cc_start: 0.6095 (mtp-110) cc_final: 0.5071 (tpt90) REVERT: B 770 LEU cc_start: 0.8395 (tp) cc_final: 0.8042 (mt) REVERT: B 795 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 1400 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7855 (t) REVERT: B 1475 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7124 (mm) REVERT: B 1496 MET cc_start: 0.7033 (tmm) cc_final: 0.6798 (tmm) REVERT: B 1528 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.6226 (ttp-170) REVERT: C 53 ARG cc_start: 0.7877 (ptm-80) cc_final: 0.7528 (ptm-80) REVERT: C 141 GLU cc_start: 0.6943 (mp0) cc_final: 0.6685 (mp0) REVERT: C 184 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7311 (p90) REVERT: C 210 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: D 132 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7277 (mp) REVERT: D 156 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.6592 (t80) REVERT: D 161 LYS cc_start: 0.7259 (mmmm) cc_final: 0.7059 (mmmm) outliers start: 55 outliers final: 33 residues processed: 225 average time/residue: 0.3400 time to fit residues: 122.9192 Evaluate side-chains 221 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 2.694 ------------------------------------------------------------------------------- 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 591 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 A residue 740 LEU Chi-restraints excluded: chain A residue 1067 TYR 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 246 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 226 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B1356 ASN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1432 GLN C 285 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.162026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123282 restraints weight = 33522.511| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 4.62 r_work: 0.3068 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23386 Z= 0.206 Angle : 0.690 13.483 31771 Z= 0.360 Chirality : 0.046 0.235 3648 Planarity : 0.005 0.064 4076 Dihedral : 6.500 76.276 3290 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.21 % Favored : 90.72 % Rotamer: Outliers : 3.12 % Allowed : 14.94 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2975 helix: 1.33 (0.14), residues: 1477 sheet: -0.76 (0.28), residues: 349 loop : -2.75 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 47 HIS 0.006 0.001 HIS C 299 PHE 0.015 0.002 PHE B1492 TYR 0.018 0.002 TYR B 954 ARG 0.004 0.001 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 1160) hydrogen bonds : angle 4.11052 ( 3384) covalent geometry : bond 0.00498 (23386) covalent geometry : angle 0.69003 (31771) *********************** 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 253 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 179 time to evaluate : 2.361 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7288 (OUTLIER) cc_final: 0.5708 (m-90) REVERT: A 377 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.6921 (p90) REVERT: A 793 LEU cc_start: 0.2613 (OUTLIER) cc_final: 0.2292 (tt) REVERT: B 518 ARG cc_start: 0.6039 (mtp-110) cc_final: 0.5002 (tpt90) REVERT: B 795 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 1294 PRO cc_start: 0.8038 (Cg_endo) cc_final: 0.7825 (Cg_endo) REVERT: B 1475 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7299 (mm) REVERT: B 1496 MET cc_start: 0.6927 (tmm) cc_final: 0.6662 (tmm) REVERT: B 1528 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.6233 (ttp-170) REVERT: C 53 ARG cc_start: 0.7866 (ptm-80) cc_final: 0.7524 (ptm-80) REVERT: C 184 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.7370 (p90) REVERT: C 187 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: C 210 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8626 (m-30) REVERT: D 50 ARG cc_start: 0.6926 (tpt170) cc_final: 0.6568 (mmp80) REVERT: D 132 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7259 (mt) REVERT: D 156 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.6819 (t80) outliers start: 74 outliers final: 43 residues processed: 236 average time/residue: 0.3697 time to fit residues: 138.3777 Evaluate side-chains 224 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 377 PHE 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 A residue 740 LEU 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 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 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 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 139 LYS 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 219 VAL Chi-restraints excluded: chain C residue 237 ASN 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 126 HIS 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 240 PHE 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 65 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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 ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1511 GLN C 285 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124460 restraints weight = 33657.728| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.79 r_work: 0.3231 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23386 Z= 0.169 Angle : 0.649 12.949 31771 Z= 0.340 Chirality : 0.044 0.220 3648 Planarity : 0.005 0.062 4076 Dihedral : 6.417 77.013 3290 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.08 % Favored : 90.89 % Rotamer: Outliers : 2.66 % Allowed : 15.53 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2975 helix: 1.41 (0.14), residues: 1479 sheet: -0.62 (0.28), residues: 346 loop : -2.74 (0.16), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 47 HIS 0.005 0.001 HIS C 299 PHE 0.014 0.002 PHE A 309 TYR 0.017 0.002 TYR A 697 ARG 0.003 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 1160) hydrogen bonds : angle 4.01927 ( 3384) covalent geometry : bond 0.00398 (23386) covalent geometry : angle 0.64877 (31771) *********************** 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 242 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6925 (ptp90) REVERT: A 307 TRP cc_start: 0.7271 (OUTLIER) cc_final: 0.5756 (m-90) REVERT: A 726 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5825 (ptt) REVERT: A 778 ASP cc_start: 0.8114 (p0) cc_final: 0.7527 (p0) REVERT: A 793 LEU cc_start: 0.2665 (OUTLIER) cc_final: 0.2323 (tt) REVERT: B 518 ARG cc_start: 0.6160 (mtp-110) cc_final: 0.5077 (tpt90) REVERT: B 657 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8170 (ptp) REVERT: B 770 LEU cc_start: 0.8423 (tp) cc_final: 0.8063 (mt) REVERT: B 795 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 1341 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6197 (mtm180) REVERT: B 1394 MET cc_start: 0.7688 (mmt) cc_final: 0.7462 (mmm) REVERT: B 1475 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7248 (mm) REVERT: B 1496 MET cc_start: 0.7054 (tmm) cc_final: 0.6793 (tmm) REVERT: B 1528 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6360 (ttp-170) REVERT: C 53 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.7526 (ptm-80) REVERT: C 141 GLU cc_start: 0.7033 (mp0) cc_final: 0.6694 (mp0) REVERT: C 184 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.7415 (p90) REVERT: C 210 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: C 285 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8370 (p0) REVERT: D 50 ARG cc_start: 0.7067 (tpt170) cc_final: 0.6718 (mmp80) REVERT: D 132 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7265 (mt) REVERT: D 156 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6822 (t80) outliers start: 63 outliers final: 42 residues processed: 223 average time/residue: 0.3496 time to fit residues: 123.3985 Evaluate side-chains 228 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 79 ARG 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 700 MET Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 740 LEU 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 878 GLU 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 1286 LEU 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 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 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 285 ASN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 126 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.1980 chunk 248 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 B1356 ASN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1511 GLN C 285 ASN ** D 126 HIS ** 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 = 0.4042 r_free = 0.4042 target = 0.166413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118401 restraints weight = 33788.892| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.45 r_work: 0.3164 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23386 Z= 0.140 Angle : 0.616 12.398 31771 Z= 0.322 Chirality : 0.042 0.208 3648 Planarity : 0.004 0.060 4076 Dihedral : 6.305 77.725 3290 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.14 % Favored : 90.82 % Rotamer: Outliers : 2.74 % Allowed : 15.66 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2975 helix: 1.57 (0.14), residues: 1479 sheet: -0.52 (0.29), residues: 338 loop : -2.72 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 47 HIS 0.004 0.001 HIS A 623 PHE 0.015 0.001 PHE B1112 TYR 0.030 0.001 TYR B 517 ARG 0.004 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 1160) hydrogen bonds : angle 3.91430 ( 3384) covalent geometry : bond 0.00316 (23386) covalent geometry : angle 0.61613 (31771) *********************** 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 242 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 2.348 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7347 (ptp90) REVERT: A 307 TRP cc_start: 0.7263 (OUTLIER) cc_final: 0.5736 (m-90) REVERT: A 726 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5777 (ptt) REVERT: A 793 LEU cc_start: 0.2668 (OUTLIER) cc_final: 0.2305 (tt) REVERT: B 518 ARG cc_start: 0.6181 (mtp-110) cc_final: 0.5074 (tpt90) REVERT: B 657 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7846 (ptp) REVERT: B 770 LEU cc_start: 0.8351 (tp) cc_final: 0.8010 (mt) REVERT: B 795 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 1400 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7814 (t) REVERT: B 1475 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7137 (mm) REVERT: B 1496 MET cc_start: 0.6951 (tmm) cc_final: 0.6672 (tmm) REVERT: B 1528 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6212 (ttp-170) REVERT: C 53 ARG cc_start: 0.7791 (ptm-80) cc_final: 0.7483 (ptm-80) REVERT: C 141 GLU cc_start: 0.6841 (mp0) cc_final: 0.6506 (mp0) REVERT: C 184 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.7343 (p90) REVERT: C 187 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: C 210 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8566 (m-30) REVERT: D 132 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7123 (mt) REVERT: D 156 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.6521 (t80) outliers start: 65 outliers final: 44 residues processed: 223 average time/residue: 0.3465 time to fit residues: 123.7201 Evaluate side-chains 230 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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 98 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 656 VAL 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 A residue 726 MET Chi-restraints excluded: chain A residue 740 LEU 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 878 GLU 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 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 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 187 GLU 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 126 HIS 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 283 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 78 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 293 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 210 optimal weight: 0.0370 chunk 177 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 279 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 HIS ** 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 ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.166393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132019 restraints weight = 33787.488| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.58 r_work: 0.3156 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 23386 Z= 0.115 Angle : 0.580 11.731 31771 Z= 0.303 Chirality : 0.041 0.192 3648 Planarity : 0.004 0.054 4076 Dihedral : 6.099 79.103 3290 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 2.11 % Allowed : 16.25 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2975 helix: 1.81 (0.14), residues: 1470 sheet: -0.41 (0.29), residues: 334 loop : -2.65 (0.16), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 47 HIS 0.004 0.001 HIS D 126 PHE 0.013 0.001 PHE D 150 TYR 0.025 0.001 TYR B 517 ARG 0.005 0.000 ARG B1341 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 1160) hydrogen bonds : angle 3.75263 ( 3384) covalent geometry : bond 0.00243 (23386) covalent geometry : angle 0.58019 (31771) ********************** 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 238 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7245 (OUTLIER) cc_final: 0.5700 (m-90) REVERT: A 726 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5859 (ptt) REVERT: A 778 ASP cc_start: 0.7835 (p0) cc_final: 0.7347 (p0) REVERT: A 793 LEU cc_start: 0.2708 (OUTLIER) cc_final: 0.2346 (tt) REVERT: A 1098 ASN cc_start: 0.6544 (t0) cc_final: 0.6033 (t0) REVERT: B 518 ARG cc_start: 0.6249 (mtp-110) cc_final: 0.5146 (tpt90) REVERT: B 657 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7974 (ptp) REVERT: B 770 LEU cc_start: 0.8270 (tp) cc_final: 0.7959 (mt) REVERT: B 795 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 1475 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7067 (mm) REVERT: B 1496 MET cc_start: 0.6901 (tmm) cc_final: 0.6588 (tmm) REVERT: B 1528 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6262 (ttp-170) REVERT: C 17 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: C 53 ARG cc_start: 0.7766 (ptm-80) cc_final: 0.7497 (ptm-80) REVERT: C 141 GLU cc_start: 0.6950 (mp0) cc_final: 0.6673 (mp0) REVERT: C 184 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.7234 (p90) REVERT: C 187 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: C 210 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8566 (m-30) REVERT: D 132 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7097 (mp) REVERT: D 156 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.6356 (t80) outliers start: 50 outliers final: 31 residues processed: 222 average time/residue: 0.4831 time to fit residues: 170.1534 Evaluate side-chains 223 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 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 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 878 GLU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1286 LEU Chi-restraints excluded: chain B residue 1356 ASN 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 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 210 ASP 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 126 HIS 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 176 ASP 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 44 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 260 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 overall best weight: 1.2146 ------------------------------------------------------------------------------- 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 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B1356 ASN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.164633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114622 restraints weight = 33612.882| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.36 r_work: 0.3135 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23386 Z= 0.194 Angle : 0.669 13.969 31771 Z= 0.349 Chirality : 0.045 0.232 3648 Planarity : 0.005 0.059 4076 Dihedral : 6.309 78.329 3290 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.24 % Allowed : 16.21 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2975 helix: 1.53 (0.14), residues: 1479 sheet: -0.49 (0.29), residues: 340 loop : -2.71 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 259 HIS 0.005 0.001 HIS C 299 PHE 0.023 0.002 PHE B1112 TYR 0.023 0.002 TYR B 517 ARG 0.003 0.001 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 1160) hydrogen bonds : angle 3.94856 ( 3384) covalent geometry : bond 0.00465 (23386) covalent geometry : angle 0.66895 (31771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14452.38 seconds wall clock time: 252 minutes 30.06 seconds (15150.06 seconds total)