Starting phenix.real_space_refine on Sun Sep 13 10:29:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdz_13928/09_2026/7qdz_13928.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 107 5.16 5 C 14295 2.51 5 N 3914 2.21 5 O 4269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9065 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 75, 'TRANS': 1093} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 8674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 8674 Classifications: {'peptide': 1145} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 24, 'TRANS': 1120} Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 5, 'PHE:plan': 5, 'ASP:plan': 6, 'TYR:plan': 8, 'GLN:plan1': 3, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 202 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: {'RNAv2': 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 chiralities: 1 Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.03, per 1000 atoms: 0.22 Number of scatterers: 22591 At special positions: 0 Unit cell: (132.787, 171.942, 171.091, 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 4269 8.00 N 3914 7.00 C 14295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5476 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 22 sheets defined 51.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.345A pdb=" N TRP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.712A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.526A pdb=" N LEU A 91 " --> pdb=" O TRP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 4.066A 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: 4.171A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 4.508A pdb=" N GLN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 3.614A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.845A 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: 3.518A pdb=" N TYR A 427 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 428 " --> pdb=" O VAL A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.026A pdb=" N TRP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.858A 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: 3.990A pdb=" N TYR A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.592A pdb=" N THR A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.061A pdb=" N ALA A 583 " --> pdb=" O CYS A 579 " (cutoff:3.500A) removed outlier: 4.116A 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 Processing helix chain 'A' and resid 618 through 631 removed outlier: 3.569A pdb=" N ARG A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 662 through 669 removed outlier: 4.136A pdb=" N VAL A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.890A pdb=" N GLN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.803A 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: 4.231A 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: 3.964A pdb=" N LYS A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.867A pdb=" N ASP A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 888 " --> pdb=" O PRO A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 888' Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 936 through 948 removed outlier: 4.282A 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: 3.542A 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 1045 removed outlier: 3.848A pdb=" N GLN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 removed outlier: 3.570A pdb=" N LEU A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1083 removed outlier: 3.947A 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: 3.825A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) removed outlier: 4.617A 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: 3.914A 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: 3.816A pdb=" N LEU A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1205 removed outlier: 4.089A pdb=" N VAL A1197 " --> pdb=" O GLU A1193 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A1205 " --> pdb=" O GLN A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1218 removed outlier: 3.516A pdb=" N SER A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A1211 " --> pdb=" O CYS A1207 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A1216 " --> pdb=" O GLY A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1230 removed outlier: 3.884A 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 421 through 436 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.615A pdb=" N CYS B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.709A pdb=" N LEU B 460 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 3.939A 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 Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 527 through 541 removed outlier: 3.743A pdb=" N LEU B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.716A pdb=" N LYS B 557 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 577 removed outlier: 4.110A pdb=" N ARG B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.556A pdb=" N ALA B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.545A pdb=" N TRP B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.688A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.887A pdb=" N VAL B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.512A pdb=" N ALA B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.685A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 3.684A pdb=" N ALA B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 726 removed outlier: 4.262A pdb=" N TRP B 717 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 removed outlier: 3.662A pdb=" N LEU B 772 " --> pdb=" O ARG B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 796 Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.510A 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: 3.649A pdb=" N TRP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 874 " --> pdb=" O LEU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 908 removed outlier: 3.849A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 removed outlier: 3.553A 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: 3.832A 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: 3.576A 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: 3.942A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1102 removed outlier: 3.730A 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 1138 through 1152 removed outlier: 3.604A pdb=" N ALA B1143 " --> pdb=" O THR B1139 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1172 removed outlier: 3.613A 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: 3.668A 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: 4.200A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1313 removed outlier: 4.041A 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 Processing helix chain 'B' and resid 1361 through 1371 removed outlier: 3.522A pdb=" N LEU B1365 " --> pdb=" O ALA B1361 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1396 Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.545A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1434 removed outlier: 3.541A pdb=" N ALA B1419 " --> pdb=" O MET B1415 " (cutoff:3.500A) Processing helix chain 'B' and resid 1436 through 1456 removed outlier: 3.795A 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 removed outlier: 3.557A pdb=" N VAL B1484 " --> pdb=" O CYS B1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 3.856A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) removed outlier: 3.572A 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 1549 Processing helix chain 'B' and resid 1552 through 1563 removed outlier: 4.116A 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: 3.705A 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 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 398 removed outlier: 8.145A pdb=" N MET A 398 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR A 358 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG A 355 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ILE A 421 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 357 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 418 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 451 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 420 " --> pdb=" O ILE A 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507 removed outlier: 6.686A pdb=" N HIS A 489 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 676 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 569 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 661 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 571 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 6.825A 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 913 through 920 removed outlier: 3.554A pdb=" N ASP A 914 " --> pdb=" O CYS A 877 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A 877 " --> pdb=" O ASP A 914 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR A 872 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 876 " --> pdb=" O LEU A 856 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU A 856 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N ASP A 878 " --> pdb=" O ASN A 854 " (cutoff:3.500A) removed outlier: 12.977A pdb=" N ASN A 854 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 843 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS A 848 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 4.371A 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: 7.003A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 25 removed outlier: 3.596A pdb=" N SER C 21 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS C 48 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.705A 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 Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.740A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.174A 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: 3.554A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP C 176 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 182 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.668A pdb=" N LEU C 205 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 215 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.362A 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: 3.554A pdb=" N ASN C 237 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.358A pdb=" N VAL D 44 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER D 59 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 46 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.984A pdb=" N LYS D 100 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 156 removed outlier: 4.019A pdb=" N ILE D 174 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS D 184 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 195 through 197 removed outlier: 4.606A pdb=" N SER D 195 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 235 through 239 removed outlier: 6.867A pdb=" N SER D 250 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 238 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL D 248 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 256 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 277 through 282 1140 hydrogen bonds defined for protein. 3321 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: 4.92 Time building geometry restraints manager: 2.60 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: 6931 1.33 - 1.46: 3981 1.46 - 1.58: 11962 1.58 - 1.70: 11 1.70 - 1.82: 168 Bond restraints: 23053 Sorted by residual: bond pdb=" SD MET C 191 " pdb=" CE MET C 191 " ideal model delta sigma weight residual 1.791 1.737 0.054 2.50e-02 1.60e+03 4.73e+00 bond pdb=" CG LEU B 688 " pdb=" CD1 LEU B 688 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.87e+00 bond pdb=" CB VAL B 973 " pdb=" CG2 VAL B 973 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.08e+00 bond pdb=" CB ILE B 968 " pdb=" CG2 ILE B 968 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" C SER B1266 " pdb=" N PRO B1267 " ideal model delta sigma weight residual 1.339 1.282 0.057 3.40e-02 8.65e+02 2.83e+00 ... (remaining 23048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 30582 2.85 - 5.71: 658 5.71 - 8.56: 57 8.56 - 11.41: 7 11.41 - 14.27: 2 Bond angle restraints: 31306 Sorted by residual: angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.25 112.05 -8.80 1.05e+00 9.07e-01 7.03e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" CB PRO A 206 " ideal model delta sigma weight residual 103.25 111.21 -7.96 1.05e+00 9.07e-01 5.75e+01 angle pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" N PRO A 162 " ideal model delta sigma weight residual 118.09 114.12 3.97 8.20e-01 1.49e+00 2.35e+01 angle pdb=" N GLU B 674 " pdb=" CA GLU B 674 " pdb=" CB GLU B 674 " ideal model delta sigma weight residual 110.16 116.28 -6.12 1.48e+00 4.57e-01 1.71e+01 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 130.57 -14.27 3.50e+00 8.16e-02 1.66e+01 ... (remaining 31301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 12376 17.59 - 35.18: 1241 35.18 - 52.77: 184 52.77 - 70.36: 52 70.36 - 87.95: 23 Dihedral angle restraints: 13876 sinusoidal: 5395 harmonic: 8481 Sorted by residual: dihedral pdb=" C4' U E 6 " pdb=" C3' U E 6 " pdb=" C2' U E 6 " pdb=" C1' U E 6 " ideal model delta sinusoidal sigma weight residual 36.35 -34.51 70.85 1 3.10e+00 1.04e-01 6.71e+02 dihedral pdb=" O4' U E 6 " pdb=" C4' U E 6 " pdb=" C3' U E 6 " pdb=" C2' U E 6 " ideal model delta sinusoidal sigma weight residual -35.15 23.34 -58.48 1 4.00e+00 6.25e-02 2.86e+02 dihedral pdb=" O4' U E 6 " pdb=" C2' U E 6 " pdb=" C1' U E 6 " pdb=" C3' U E 6 " ideal model delta sinusoidal sigma weight residual -94.41 -34.82 -59.58 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 13873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2529 0.053 - 0.107: 853 0.107 - 0.160: 168 0.160 - 0.214: 23 0.214 - 0.267: 10 Chirality restraints: 3583 Sorted by residual: chirality pdb=" C2' U E 6 " pdb=" C3' U E 6 " pdb=" O2' U E 6 " pdb=" C1' U E 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU A 628 " pdb=" CB LEU A 628 " pdb=" CD1 LEU A 628 " pdb=" CD2 LEU A 628 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU C 43 " pdb=" CB LEU C 43 " pdb=" CD1 LEU C 43 " pdb=" CD2 LEU C 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3580 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 640 " -0.082 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO A 641 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1463 " -0.030 2.00e-02 2.50e+03 2.89e-02 2.09e+01 pdb=" CG TRP B1463 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP B1463 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B1463 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1463 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1463 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1463 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1463 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1463 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B1463 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A1180 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A1181 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A1181 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1181 " 0.052 5.00e-02 4.00e+02 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 228 2.53 - 3.12: 18653 3.12 - 3.72: 35302 3.72 - 4.31: 47227 4.31 - 4.90: 79446 Nonbonded interactions: 180856 Sorted by model distance: nonbonded pdb=" OG SER C 251 " pdb=" OD1 ASP C 253 " model vdw 1.941 3.040 nonbonded pdb=" O ALA A 666 " pdb=" NH1 ARG A 703 " model vdw 2.042 3.120 nonbonded pdb=" OE1 GLU A 23 " pdb=" OG SER A 41 " model vdw 2.051 3.040 nonbonded pdb=" O THR B1392 " pdb=" OG SER B1395 " model vdw 2.070 3.040 nonbonded pdb=" NH1 ARG A 576 " pdb=" OP1 U E 2 " model vdw 2.088 3.120 ... (remaining 180851 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.150 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.007 0.074 23053 Z= 0.306 Angle : 0.984 14.268 31306 Z= 0.538 Chirality : 0.055 0.267 3583 Planarity : 0.007 0.124 4009 Dihedral : 14.625 87.948 8400 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 2908 helix: 0.90 (0.14), residues: 1405 sheet: -1.74 (0.26), residues: 349 loop : -3.25 (0.15), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1039 TYR 0.041 0.003 TYR B 517 PHE 0.049 0.003 PHE A 665 TRP 0.077 0.003 TRP B1463 HIS 0.013 0.002 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.31 (23053) covalent geometry : angle 0.98425 / 0.54 (31306) hydrogen bonds : bond 0.15797 / 10.73 ( 1140) hydrogen bonds : angle 6.26578 / 4.40 ( 3321) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.6923 (p0) cc_final: 0.6523 (p0) REVERT: A 490 TYR cc_start: 0.8149 (m-80) cc_final: 0.7744 (m-80) REVERT: A 671 MET cc_start: 0.5113 (tpt) cc_final: 0.4650 (ttt) REVERT: A 734 MET cc_start: 0.8665 (tmm) cc_final: 0.8144 (tmm) REVERT: A 1193 GLU cc_start: 0.5640 (mp0) cc_final: 0.4984 (mp0) REVERT: B 1023 ILE cc_start: 0.9125 (mm) cc_final: 0.8910 (mm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1408 time to fit residues: 43.3607 Evaluate side-chains 136 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.0670 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 333 HIS A 500 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN A1133 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 HIS ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1462 HIS B1558 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.095656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071014 restraints weight = 89933.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.072714 restraints weight = 46261.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.073910 restraints weight = 30094.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074628 restraints weight = 22904.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074998 restraints weight = 19346.487| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23053 Z= 0.140 Angle : 0.708 12.538 31306 Z= 0.362 Chirality : 0.044 0.220 3583 Planarity : 0.005 0.068 4009 Dihedral : 5.751 75.855 3201 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.12 % Favored : 91.85 % Rotamer: Outliers : 0.59 % Allowed : 7.77 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2908 helix: 1.27 (0.14), residues: 1426 sheet: -1.38 (0.29), residues: 314 loop : -2.91 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 576 TYR 0.028 0.002 TYR B 517 PHE 0.031 0.002 PHE B1316 TRP 0.034 0.002 TRP B1463 HIS 0.007 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (23053) covalent geometry : angle 0.70841 / 0.36 (31306) hydrogen bonds : bond 0.04835 / 3.24 ( 1140) hydrogen bonds : angle 4.72918 / 3.30 ( 3321) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7450 (mp0) REVERT: A 101 ASP cc_start: 0.6883 (p0) cc_final: 0.6405 (p0) REVERT: A 490 TYR cc_start: 0.8025 (m-80) cc_final: 0.7575 (m-80) REVERT: A 671 MET cc_start: 0.4593 (tpt) cc_final: 0.4273 (ttt) REVERT: A 726 MET cc_start: 0.5103 (ppp) cc_final: 0.4668 (tmm) REVERT: A 734 MET cc_start: 0.8734 (tmm) cc_final: 0.8320 (tmm) REVERT: A 1193 GLU cc_start: 0.5897 (mp0) cc_final: 0.5281 (mp0) REVERT: B 551 LEU cc_start: 0.9335 (mt) cc_final: 0.9010 (pp) outliers start: 14 outliers final: 5 residues processed: 194 average time/residue: 0.1387 time to fit residues: 45.4123 Evaluate side-chains 151 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 206 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN A 148 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1462 HIS B1559 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.093046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068040 restraints weight = 90895.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069738 restraints weight = 47668.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070967 restraints weight = 31563.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071683 restraints weight = 24184.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.072051 restraints weight = 20492.819| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23053 Z= 0.195 Angle : 0.692 12.878 31306 Z= 0.357 Chirality : 0.044 0.235 3583 Planarity : 0.005 0.063 4009 Dihedral : 5.686 77.274 3201 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.22 % Favored : 91.75 % Rotamer: Outliers : 1.52 % Allowed : 11.61 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2908 helix: 1.36 (0.14), residues: 1424 sheet: -1.30 (0.28), residues: 344 loop : -2.75 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1528 TYR 0.022 0.002 TYR B 954 PHE 0.023 0.002 PHE A1020 TRP 0.014 0.002 TRP B1436 HIS 0.008 0.001 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (23053) covalent geometry : angle 0.69227 / 0.36 (31306) hydrogen bonds : bond 0.04622 / 3.09 ( 1140) hydrogen bonds : angle 4.56705 / 3.19 ( 3321) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7038 (p0) cc_final: 0.6667 (p0) REVERT: A 490 TYR cc_start: 0.8024 (m-80) cc_final: 0.7728 (m-80) REVERT: A 645 GLU cc_start: 0.6710 (pt0) cc_final: 0.6498 (pt0) REVERT: A 671 MET cc_start: 0.4742 (tpt) cc_final: 0.4347 (ttt) REVERT: A 681 MET cc_start: 0.5530 (tpp) cc_final: 0.5286 (tpp) REVERT: A 726 MET cc_start: 0.4817 (ppp) cc_final: 0.4222 (tmm) REVERT: A 734 MET cc_start: 0.8749 (tmm) cc_final: 0.8234 (tmm) REVERT: A 822 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8725 (mp10) REVERT: A 1193 GLU cc_start: 0.6064 (mp0) cc_final: 0.5492 (mp0) REVERT: B 803 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8236 (pp) REVERT: C 51 ASP cc_start: 0.7618 (p0) cc_final: 0.7135 (p0) outliers start: 36 outliers final: 16 residues processed: 177 average time/residue: 0.1399 time to fit residues: 42.2540 Evaluate side-chains 156 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1511 GLN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 0.9990 chunk 267 optimal weight: 0.5980 chunk 263 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 HIS A1032 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1462 HIS ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.093941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.069044 restraints weight = 90239.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.070858 restraints weight = 46886.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.072069 restraints weight = 30601.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.072862 restraints weight = 23352.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.073241 restraints weight = 19744.021| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23053 Z= 0.133 Angle : 0.635 15.591 31306 Z= 0.324 Chirality : 0.042 0.181 3583 Planarity : 0.004 0.058 4009 Dihedral : 5.480 79.889 3201 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.03 % Allowed : 13.76 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2908 helix: 1.56 (0.14), residues: 1421 sheet: -1.14 (0.29), residues: 327 loop : -2.65 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1417 TYR 0.018 0.001 TYR B 517 PHE 0.032 0.001 PHE B1316 TRP 0.015 0.001 TRP B1436 HIS 0.005 0.001 HIS A 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23053) covalent geometry : angle 0.63476 / 0.32 (31306) hydrogen bonds : bond 0.03876 / 2.60 ( 1140) hydrogen bonds : angle 4.26689 / 2.97 ( 3321) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TYR cc_start: 0.7631 (m-80) cc_final: 0.7394 (m-80) REVERT: A 490 TYR cc_start: 0.7995 (m-80) cc_final: 0.7754 (m-80) REVERT: A 646 ILE cc_start: 0.8462 (pt) cc_final: 0.8090 (tp) REVERT: A 671 MET cc_start: 0.4438 (tpt) cc_final: 0.4035 (ttt) REVERT: A 726 MET cc_start: 0.4670 (ppp) cc_final: 0.4162 (tmm) REVERT: A 734 MET cc_start: 0.8750 (tmm) cc_final: 0.8288 (tmm) REVERT: A 822 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8682 (mp10) REVERT: A 1193 GLU cc_start: 0.5992 (mp0) cc_final: 0.5454 (mp0) REVERT: B 803 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8199 (pp) REVERT: B 1475 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9137 (pp) REVERT: B 1559 GLN cc_start: 0.8829 (mm110) cc_final: 0.8317 (pp30) REVERT: C 1 MET cc_start: 0.5348 (tpt) cc_final: 0.4846 (tpt) REVERT: C 51 ASP cc_start: 0.7608 (p0) cc_final: 0.7187 (p0) outliers start: 48 outliers final: 19 residues processed: 193 average time/residue: 0.1365 time to fit residues: 45.0183 Evaluate side-chains 162 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1511 GLN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 62 optimal weight: 20.0000 chunk 279 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 chunk 267 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 317 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1462 HIS ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3923 r_free = 0.3923 target = 0.093383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068317 restraints weight = 90514.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070020 restraints weight = 47499.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071319 restraints weight = 31240.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.072069 restraints weight = 23894.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072432 restraints weight = 20254.459| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23053 Z= 0.151 Angle : 0.643 13.696 31306 Z= 0.327 Chirality : 0.042 0.342 3583 Planarity : 0.005 0.066 4009 Dihedral : 5.441 81.066 3201 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.45 % Allowed : 14.61 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2908 helix: 1.59 (0.14), residues: 1421 sheet: -1.00 (0.28), residues: 329 loop : -2.62 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 703 TYR 0.034 0.001 TYR B 517 PHE 0.016 0.001 PHE A1020 TRP 0.028 0.001 TRP C 47 HIS 0.016 0.001 HIS B1462 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (23053) covalent geometry : angle 0.64294 / 0.33 (31306) hydrogen bonds : bond 0.03899 / 2.62 ( 1140) hydrogen bonds : angle 4.22113 / 2.94 ( 3321) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6847 (OUTLIER) cc_final: 0.6556 (m-90) REVERT: A 671 MET cc_start: 0.4692 (tpt) cc_final: 0.4437 (tpp) REVERT: A 726 MET cc_start: 0.4701 (ppp) cc_final: 0.4186 (tmm) REVERT: A 734 MET cc_start: 0.8775 (tmm) cc_final: 0.8303 (tmm) REVERT: A 822 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: A 1091 LEU cc_start: 0.8426 (mm) cc_final: 0.8176 (mp) REVERT: A 1193 GLU cc_start: 0.5992 (mp0) cc_final: 0.5496 (mp0) REVERT: B 517 TYR cc_start: 0.7568 (m-80) cc_final: 0.7181 (m-80) REVERT: B 591 LEU cc_start: 0.8512 (mt) cc_final: 0.7935 (pp) REVERT: B 803 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8228 (pp) REVERT: B 886 MET cc_start: 0.8335 (tmm) cc_final: 0.8080 (tmm) REVERT: B 1475 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9142 (pp) REVERT: B 1559 GLN cc_start: 0.8857 (mm110) cc_final: 0.8252 (pp30) REVERT: C 1 MET cc_start: 0.5421 (tpt) cc_final: 0.4960 (tpt) REVERT: C 51 ASP cc_start: 0.7583 (p0) cc_final: 0.7087 (p0) REVERT: C 191 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8407 (mtm) REVERT: D 143 SER cc_start: 0.8657 (t) cc_final: 0.8309 (p) outliers start: 58 outliers final: 31 residues processed: 190 average time/residue: 0.1344 time to fit residues: 43.4188 Evaluate side-chains 174 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 141 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 23 optimal weight: 0.0270 chunk 278 optimal weight: 20.0000 chunk 284 optimal weight: 3.9990 overall best weight: 3.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 HIS ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1356 ASN B1462 HIS ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1564 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.091789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066683 restraints weight = 91153.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.068337 restraints weight = 48261.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.069494 restraints weight = 31662.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070162 restraints weight = 24373.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070502 restraints weight = 20717.143| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23053 Z= 0.215 Angle : 0.687 14.695 31306 Z= 0.352 Chirality : 0.044 0.208 3583 Planarity : 0.005 0.055 4009 Dihedral : 5.588 82.736 3201 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.20 % Allowed : 15.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2908 helix: 1.46 (0.14), residues: 1431 sheet: -1.09 (0.28), residues: 338 loop : -2.66 (0.16), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 703 TYR 0.029 0.002 TYR B 517 PHE 0.030 0.002 PHE B1316 TRP 0.020 0.002 TRP C 49 HIS 0.014 0.001 HIS B1462 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (23053) covalent geometry : angle 0.68706 / 0.35 (31306) hydrogen bonds : bond 0.04312 / 2.88 ( 1140) hydrogen bonds : angle 4.35650 / 3.03 ( 3321) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.4941 (tpt) cc_final: 0.4679 (tpp) REVERT: A 726 MET cc_start: 0.4791 (ppp) cc_final: 0.4490 (tmm) REVERT: A 734 MET cc_start: 0.8781 (tmm) cc_final: 0.8312 (tmm) REVERT: A 822 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8638 (mp10) REVERT: A 1193 GLU cc_start: 0.6093 (mp0) cc_final: 0.5631 (mp0) REVERT: B 517 TYR cc_start: 0.7488 (m-80) cc_final: 0.7151 (m-80) REVERT: B 541 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6369 (tt) REVERT: B 591 LEU cc_start: 0.8595 (mt) cc_final: 0.8042 (pp) REVERT: B 803 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8355 (pp) REVERT: B 886 MET cc_start: 0.8426 (tmm) cc_final: 0.8158 (tmm) REVERT: B 1475 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9143 (pp) REVERT: B 1559 GLN cc_start: 0.8937 (mm110) cc_final: 0.8244 (pp30) REVERT: C 1 MET cc_start: 0.5484 (tpt) cc_final: 0.5050 (tpt) REVERT: C 51 ASP cc_start: 0.7677 (p0) cc_final: 0.7223 (p0) REVERT: C 191 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8480 (mtm) REVERT: D 143 SER cc_start: 0.8701 (t) cc_final: 0.8378 (p) outliers start: 52 outliers final: 35 residues processed: 180 average time/residue: 0.1278 time to fit residues: 39.9136 Evaluate side-chains 172 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1356 ASN Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1475 LEU Chi-restraints excluded: chain B residue 1477 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 172 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 175 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 126 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1462 HIS ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.093566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068644 restraints weight = 90288.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070370 restraints weight = 47132.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071639 restraints weight = 30951.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.072320 restraints weight = 23587.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.072889 restraints weight = 19959.623| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23053 Z= 0.123 Angle : 0.630 12.555 31306 Z= 0.319 Chirality : 0.042 0.401 3583 Planarity : 0.004 0.054 4009 Dihedral : 5.403 84.672 3201 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.94 % Allowed : 17.18 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.16), residues: 2908 helix: 1.67 (0.14), residues: 1422 sheet: -0.87 (0.29), residues: 328 loop : -2.58 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 703 TYR 0.026 0.001 TYR B 517 PHE 0.014 0.001 PHE A 377 TRP 0.025 0.001 TRP A 307 HIS 0.013 0.001 HIS B1462 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (23053) covalent geometry : angle 0.63036 / 0.32 (31306) hydrogen bonds : bond 0.03656 / 2.46 ( 1140) hydrogen bonds : angle 4.09399 / 2.84 ( 3321) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8000 (tmm) cc_final: 0.7552 (ttt) REVERT: A 726 MET cc_start: 0.4597 (ppp) cc_final: 0.4092 (tmm) REVERT: A 734 MET cc_start: 0.8755 (tmm) cc_final: 0.8384 (tmm) REVERT: A 822 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: A 1193 GLU cc_start: 0.5842 (mp0) cc_final: 0.5447 (mp0) REVERT: B 517 TYR cc_start: 0.7536 (m-80) cc_final: 0.6930 (m-80) REVERT: B 541 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6181 (tt) REVERT: B 591 LEU cc_start: 0.8480 (mt) cc_final: 0.7978 (pp) REVERT: B 803 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8354 (pp) REVERT: B 886 MET cc_start: 0.8440 (tmm) cc_final: 0.8192 (tmm) REVERT: B 992 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8149 (t-90) REVERT: B 1559 GLN cc_start: 0.8931 (mm110) cc_final: 0.8242 (pp30) REVERT: C 1 MET cc_start: 0.5209 (tpt) cc_final: 0.4863 (tpt) REVERT: C 51 ASP cc_start: 0.7623 (p0) cc_final: 0.7194 (p0) REVERT: C 136 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 191 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8420 (mtm) REVERT: D 143 SER cc_start: 0.8707 (t) cc_final: 0.8379 (p) outliers start: 46 outliers final: 29 residues processed: 183 average time/residue: 0.1391 time to fit residues: 43.0332 Evaluate side-chains 173 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 224 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 257 optimal weight: 0.0570 chunk 215 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 274 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.092372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067222 restraints weight = 90306.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.068991 restraints weight = 47462.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070056 restraints weight = 31296.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070919 restraints weight = 24089.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071244 restraints weight = 20536.431| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23053 Z= 0.170 Angle : 0.663 15.214 31306 Z= 0.334 Chirality : 0.043 0.404 3583 Planarity : 0.004 0.052 4009 Dihedral : 5.435 85.750 3201 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.24 % Allowed : 17.39 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2908 helix: 1.60 (0.14), residues: 1432 sheet: -1.00 (0.28), residues: 338 loop : -2.61 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 703 TYR 0.024 0.002 TYR B 517 PHE 0.020 0.002 PHE B1316 TRP 0.018 0.001 TRP C 49 HIS 0.010 0.001 HIS B1462 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (23053) covalent geometry : angle 0.66280 / 0.33 (31306) hydrogen bonds : bond 0.03930 / 2.63 ( 1140) hydrogen bonds : angle 4.16290 / 2.89 ( 3321) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 MET cc_start: 0.4670 (ppp) cc_final: 0.4390 (tmm) REVERT: A 734 MET cc_start: 0.8804 (tmm) cc_final: 0.8372 (tmm) REVERT: A 822 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8684 (mp10) REVERT: A 1193 GLU cc_start: 0.5952 (mp0) cc_final: 0.5563 (mp0) REVERT: B 517 TYR cc_start: 0.7498 (m-80) cc_final: 0.6924 (m-80) REVERT: B 591 LEU cc_start: 0.8524 (mt) cc_final: 0.8014 (pp) REVERT: B 803 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8423 (pp) REVERT: B 886 MET cc_start: 0.8469 (tmm) cc_final: 0.8163 (tmm) REVERT: B 992 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8143 (t-90) REVERT: C 1 MET cc_start: 0.5200 (tpt) cc_final: 0.4874 (tpt) REVERT: C 51 ASP cc_start: 0.7661 (p0) cc_final: 0.7213 (p0) REVERT: C 191 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8442 (mtm) REVERT: D 143 SER cc_start: 0.8720 (t) cc_final: 0.8433 (p) outliers start: 53 outliers final: 38 residues processed: 182 average time/residue: 0.1395 time to fit residues: 43.4660 Evaluate side-chains 174 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1356 ASN Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 231 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 203 optimal weight: 0.0070 chunk 41 optimal weight: 8.9990 chunk 153 optimal weight: 0.0970 chunk 243 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1462 HIS ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.092060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066867 restraints weight = 91315.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.068539 restraints weight = 48041.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069817 restraints weight = 31718.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070557 restraints weight = 24385.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.070824 restraints weight = 20726.162| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23053 Z= 0.180 Angle : 0.678 13.464 31306 Z= 0.343 Chirality : 0.043 0.403 3583 Planarity : 0.004 0.052 4009 Dihedral : 5.505 87.057 3201 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.07 % Allowed : 17.77 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2908 helix: 1.54 (0.14), residues: 1437 sheet: -1.06 (0.27), residues: 350 loop : -2.62 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 703 TYR 0.023 0.002 TYR B 517 PHE 0.014 0.002 PHE A1020 TRP 0.018 0.001 TRP C 49 HIS 0.006 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (23053) covalent geometry : angle 0.67772 / 0.34 (31306) hydrogen bonds : bond 0.04032 / 2.71 ( 1140) hydrogen bonds : angle 4.19945 / 2.92 ( 3321) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 MET cc_start: 0.4682 (ppp) cc_final: 0.4377 (tmm) REVERT: A 734 MET cc_start: 0.8810 (tmm) cc_final: 0.8383 (tmm) REVERT: A 822 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: A 1096 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: A 1193 GLU cc_start: 0.6003 (mp0) cc_final: 0.5624 (mp0) REVERT: B 591 LEU cc_start: 0.8548 (mt) cc_final: 0.8065 (pp) REVERT: B 803 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8444 (pp) REVERT: B 886 MET cc_start: 0.8485 (tmm) cc_final: 0.8203 (tmm) REVERT: B 992 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8132 (t-90) REVERT: C 1 MET cc_start: 0.5166 (tpt) cc_final: 0.4842 (tpt) REVERT: C 51 ASP cc_start: 0.7683 (p0) cc_final: 0.7280 (p0) REVERT: C 191 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: D 143 SER cc_start: 0.8686 (t) cc_final: 0.8388 (p) outliers start: 49 outliers final: 38 residues processed: 171 average time/residue: 0.1331 time to fit residues: 39.3453 Evaluate side-chains 175 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 63 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 121 optimal weight: 50.0000 chunk 108 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.091654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066452 restraints weight = 91512.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.068120 restraints weight = 48237.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.069375 restraints weight = 31861.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.070099 restraints weight = 24386.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070500 restraints weight = 20763.209| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23053 Z= 0.193 Angle : 0.694 15.243 31306 Z= 0.349 Chirality : 0.044 0.409 3583 Planarity : 0.005 0.052 4009 Dihedral : 5.556 88.408 3201 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.07 % Allowed : 18.24 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2908 helix: 1.51 (0.14), residues: 1437 sheet: -1.06 (0.27), residues: 350 loop : -2.62 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 703 TYR 0.019 0.002 TYR B 972 PHE 0.014 0.002 PHE A1020 TRP 0.017 0.001 TRP C 49 HIS 0.010 0.001 HIS B1462 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (23053) covalent geometry : angle 0.69412 / 0.35 (31306) hydrogen bonds : bond 0.04096 / 2.75 ( 1140) hydrogen bonds : angle 4.24491 / 2.95 ( 3321) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ILE cc_start: 0.8429 (pt) cc_final: 0.8135 (tp) REVERT: A 726 MET cc_start: 0.4733 (ppp) cc_final: 0.4410 (tmm) REVERT: A 734 MET cc_start: 0.8795 (tmm) cc_final: 0.8369 (tmm) REVERT: A 822 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: A 1096 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: A 1193 GLU cc_start: 0.6016 (mp0) cc_final: 0.5642 (mp0) REVERT: B 591 LEU cc_start: 0.8566 (mt) cc_final: 0.8084 (pp) REVERT: B 886 MET cc_start: 0.8487 (tmm) cc_final: 0.8210 (tmm) REVERT: B 992 HIS cc_start: 0.8531 (OUTLIER) cc_final: 0.8124 (t-90) REVERT: C 1 MET cc_start: 0.5206 (tpt) cc_final: 0.4906 (tpt) REVERT: C 191 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8436 (mtm) REVERT: D 143 SER cc_start: 0.8682 (t) cc_final: 0.8398 (p) outliers start: 49 outliers final: 41 residues processed: 170 average time/residue: 0.1378 time to fit residues: 39.8785 Evaluate side-chains 178 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1462 HIS Chi-restraints excluded: chain B residue 1547 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 267 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 78 optimal weight: 0.0270 chunk 70 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 266 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1462 HIS ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.092940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068126 restraints weight = 90552.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.069813 restraints weight = 47218.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071075 restraints weight = 30984.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071808 restraints weight = 23661.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.072216 restraints weight = 20051.902| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23053 Z= 0.128 Angle : 0.647 14.272 31306 Z= 0.324 Chirality : 0.042 0.411 3583 Planarity : 0.004 0.050 4009 Dihedral : 5.388 89.575 3201 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.77 % Allowed : 18.36 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2908 helix: 1.70 (0.14), residues: 1431 sheet: -0.92 (0.28), residues: 342 loop : -2.61 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 703 TYR 0.040 0.001 TYR B 517 PHE 0.048 0.001 PHE B1316 TRP 0.015 0.001 TRP C 47 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (23053) covalent geometry : angle 0.64688 / 0.32 (31306) hydrogen bonds : bond 0.03554 / 2.40 ( 1140) hydrogen bonds : angle 4.03087 / 2.80 ( 3321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4679.67 seconds wall clock time: 82 minutes 12.97 seconds (4932.97 seconds total)