Starting phenix.real_space_refine on Thu Jun 19 17:18:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qdz_13928/06_2025/7qdz_13928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qdz_13928/06_2025/7qdz_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_13928/06_2025/7qdz_13928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qdz_13928/06_2025/7qdz_13928.map" model { file = "/net/cci-nas-00/data/ceres_data/7qdz_13928/06_2025/7qdz_13928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qdz_13928/06_2025/7qdz_13928.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 107 5.16 5 C 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 8, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 8, 'HIS:plan': 5} 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: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 12 Time building chain proxies: 12.86, per 1000 atoms: 0.57 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: 6.25 Conformation dependent library (CDL) restraints added in 3.0 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: 2.51 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: 8.78 Time building geometry restraints manager: 7.32 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: 30592 2.85 - 5.71: 648 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: 12389 17.59 - 35.18: 1242 35.18 - 52.77: 188 52.77 - 70.36: 57 70.36 - 87.95: 22 Dihedral angle restraints: 13898 sinusoidal: 5417 harmonic: 8481 Sorted by residual: dihedral pdb=" CA LEU A 586 " pdb=" C LEU A 586 " pdb=" N THR A 587 " pdb=" CA THR A 587 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N LYS C 140 " pdb=" CA LYS C 140 " ideal model delta harmonic sigma weight residual 180.00 153.79 26.21 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 13895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2529 0.053 - 0.106: 860 0.106 - 0.160: 166 0.160 - 0.213: 22 0.213 - 0.266: 6 Chirality restraints: 3583 Sorted by residual: 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 chirality pdb=" CG LEU C 84 " pdb=" CB LEU C 84 " pdb=" CD1 LEU C 84 " pdb=" CD2 LEU C 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 51.500 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.982 14.268 31306 Z= 0.539 Chirality : 0.054 0.266 3583 Planarity : 0.007 0.124 4009 Dihedral : 14.683 87.948 8422 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (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 TRP 0.077 0.003 TRP B1463 HIS 0.013 0.002 HIS A 636 PHE 0.049 0.003 PHE A 665 TYR 0.041 0.003 TYR B 517 ARG 0.012 0.001 ARG A1039 Details of bonding type rmsd hydrogen bonds : bond 0.15797 ( 1140) hydrogen bonds : angle 6.26578 ( 3321) covalent geometry : bond 0.00686 (23053) covalent geometry : angle 0.98161 (31306) *********************** 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 : 2.377 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: 0.2940 time to fit residues: 89.0535 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 : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 121 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 263 optimal weight: 0.0980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** B1154 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 ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.093643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068726 restraints weight = 90303.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070395 restraints weight = 47008.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071537 restraints weight = 30977.824| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23053 Z= 0.182 Angle : 0.713 12.717 31306 Z= 0.371 Chirality : 0.044 0.216 3583 Planarity : 0.006 0.074 4009 Dihedral : 6.664 76.676 3223 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.56 % Favored : 91.40 % Rotamer: Outliers : 0.68 % Allowed : 8.99 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 2908 helix: 1.16 (0.14), residues: 1428 sheet: -1.42 (0.28), residues: 332 loop : -2.91 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1463 HIS 0.009 0.001 HIS A 636 PHE 0.031 0.002 PHE B1316 TYR 0.029 0.002 TYR B 517 ARG 0.007 0.001 ARG A 606 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 1140) hydrogen bonds : angle 4.82409 ( 3321) covalent geometry : bond 0.00402 (23053) covalent geometry : angle 0.71343 (31306) *********************** 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 179 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 2.560 Fit side-chains REVERT: A 101 ASP cc_start: 0.7105 (p0) cc_final: 0.6634 (p0) REVERT: A 490 TYR cc_start: 0.8015 (m-80) cc_final: 0.7678 (m-80) REVERT: A 671 MET cc_start: 0.4650 (tpt) cc_final: 0.4338 (ttt) REVERT: A 681 MET cc_start: 0.6512 (mmp) cc_final: 0.6258 (tpp) REVERT: A 726 MET cc_start: 0.5051 (ppp) cc_final: 0.4612 (tmm) REVERT: A 734 MET cc_start: 0.8778 (tmm) cc_final: 0.8321 (tmm) REVERT: A 822 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8654 (mp10) REVERT: A 1193 GLU cc_start: 0.6033 (mp0) cc_final: 0.5372 (mp0) outliers start: 16 outliers final: 7 residues processed: 172 average time/residue: 0.2867 time to fit residues: 83.8717 Evaluate side-chains 145 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain B residue 572 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 21 SER 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 196 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN A 148 ASN A 317 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 HIS ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN B 942 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.092064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066931 restraints weight = 90443.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.068502 restraints weight = 47698.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069814 restraints weight = 31933.987| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23053 Z= 0.212 Angle : 0.706 12.670 31306 Z= 0.366 Chirality : 0.044 0.239 3583 Planarity : 0.005 0.065 4009 Dihedral : 6.622 79.510 3223 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.56 % Favored : 91.40 % Rotamer: Outliers : 2.15 % Allowed : 12.62 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2908 helix: 1.23 (0.14), residues: 1428 sheet: -1.30 (0.28), residues: 325 loop : -2.82 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 49 HIS 0.011 0.002 HIS B1462 PHE 0.024 0.002 PHE A1020 TYR 0.035 0.002 TYR D 162 ARG 0.005 0.001 ARG B1528 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 1140) hydrogen bonds : angle 4.64867 ( 3321) covalent geometry : bond 0.00477 (23053) covalent geometry : angle 0.70605 (31306) *********************** 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 201 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 2.411 Fit side-chains revert: symmetry clash REVERT: A 490 TYR cc_start: 0.8012 (m-80) cc_final: 0.7807 (m-80) REVERT: A 671 MET cc_start: 0.4659 (tpt) cc_final: 0.4336 (ttt) REVERT: A 726 MET cc_start: 0.4842 (ppp) cc_final: 0.4528 (tmm) REVERT: A 734 MET cc_start: 0.8809 (tmm) cc_final: 0.8302 (tmm) REVERT: A 1084 MET cc_start: 0.7166 (tpp) cc_final: 0.6952 (tpp) REVERT: A 1193 GLU cc_start: 0.6201 (mp0) cc_final: 0.5583 (mp0) REVERT: B 803 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8279 (pp) REVERT: B 886 MET cc_start: 0.8421 (tmm) cc_final: 0.8130 (tmm) REVERT: B 1475 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9155 (pp) REVERT: C 1 MET cc_start: 0.5510 (tpt) cc_final: 0.4880 (tpt) outliers start: 51 outliers final: 19 residues processed: 189 average time/residue: 0.2800 time to fit residues: 90.1687 Evaluate side-chains 156 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 611 LEU 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 1289 VAL 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 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 189 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 203 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 285 optimal weight: 0.0980 chunk 165 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 0.0870 chunk 202 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 overall best weight: 0.6376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN ** B1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1462 HIS ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1564 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.094494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069668 restraints weight = 90526.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.071472 restraints weight = 46760.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072766 restraints weight = 30378.727| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23053 Z= 0.117 Angle : 0.623 14.776 31306 Z= 0.319 Chirality : 0.041 0.189 3583 Planarity : 0.004 0.059 4009 Dihedral : 6.298 82.136 3223 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.77 % Allowed : 14.52 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2908 helix: 1.52 (0.14), residues: 1424 sheet: -1.17 (0.28), residues: 329 loop : -2.64 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1436 HIS 0.004 0.001 HIS B1462 PHE 0.029 0.001 PHE B1316 TYR 0.031 0.001 TYR B 517 ARG 0.004 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 1140) hydrogen bonds : angle 4.23713 ( 3321) covalent geometry : bond 0.00247 (23053) covalent geometry : angle 0.62287 (31306) *********************** 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 209 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 TYR cc_start: 0.7938 (m-80) cc_final: 0.7706 (m-80) REVERT: A 646 ILE cc_start: 0.8441 (pt) cc_final: 0.8101 (tp) REVERT: A 671 MET cc_start: 0.4398 (tpt) cc_final: 0.3903 (tpp) REVERT: A 726 MET cc_start: 0.4575 (ppp) cc_final: 0.4057 (tmm) REVERT: A 734 MET cc_start: 0.8719 (tmm) cc_final: 0.8343 (tmm) REVERT: A 822 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: A 1193 GLU cc_start: 0.6025 (mp0) cc_final: 0.5493 (mp0) REVERT: B 803 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8247 (pp) REVERT: B 1559 GLN cc_start: 0.8927 (mm110) cc_final: 0.8231 (pp30) REVERT: C 1 MET cc_start: 0.5281 (tpt) cc_final: 0.5010 (tpt) REVERT: C 51 ASP cc_start: 0.7678 (p0) cc_final: 0.7252 (p0) outliers start: 42 outliers final: 16 residues processed: 199 average time/residue: 0.2926 time to fit residues: 98.5044 Evaluate side-chains 162 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 452 LEU 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 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 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 D residue 1 MET Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 261 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 22 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 245 optimal weight: 0.3980 chunk 280 optimal weight: 9.9990 overall best weight: 1.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** 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** ** 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 = 0.3936 r_free = 0.3936 target = 0.094017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069160 restraints weight = 90938.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070880 restraints weight = 47397.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.072160 restraints weight = 30988.629| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23053 Z= 0.127 Angle : 0.622 13.533 31306 Z= 0.317 Chirality : 0.041 0.336 3583 Planarity : 0.004 0.059 4009 Dihedral : 6.165 82.900 3223 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.49 % Allowed : 15.28 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2908 helix: 1.66 (0.14), residues: 1417 sheet: -1.06 (0.29), residues: 321 loop : -2.57 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1463 HIS 0.015 0.001 HIS B1462 PHE 0.015 0.001 PHE A 296 TYR 0.016 0.001 TYR D 162 ARG 0.004 0.000 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 1140) hydrogen bonds : angle 4.12836 ( 3321) covalent geometry : bond 0.00283 (23053) covalent geometry : angle 0.62181 (31306) *********************** 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 211 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 TRP cc_start: 0.6876 (OUTLIER) cc_final: 0.6568 (m-90) REVERT: A 646 ILE cc_start: 0.8447 (pt) cc_final: 0.8139 (tp) REVERT: A 671 MET cc_start: 0.4800 (tpt) cc_final: 0.4536 (tpp) REVERT: A 726 MET cc_start: 0.4581 (ppp) cc_final: 0.4049 (tmm) REVERT: A 734 MET cc_start: 0.8742 (tmm) cc_final: 0.8317 (tmm) REVERT: A 822 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8676 (mp10) REVERT: A 1193 GLU cc_start: 0.6053 (mp0) cc_final: 0.5581 (mp0) REVERT: B 541 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6271 (tt) REVERT: B 591 LEU cc_start: 0.8446 (mt) cc_final: 0.7930 (pp) REVERT: B 803 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8267 (pp) REVERT: C 1 MET cc_start: 0.5148 (tpt) cc_final: 0.4938 (tpt) REVERT: C 136 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 143 SER cc_start: 0.8669 (t) cc_final: 0.8319 (p) outliers start: 59 outliers final: 31 residues processed: 199 average time/residue: 0.3021 time to fit residues: 101.2924 Evaluate side-chains 178 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 587 THR 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 783 GLU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1069 ASP 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 803 LEU Chi-restraints excluded: chain B residue 913 THR 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 C residue 34 THR Chi-restraints excluded: chain C residue 184 HIS 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 44 VAL 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 120 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 230 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS ** 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** B1558 ASN ** 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 = 0.3901 r_free = 0.3901 target = 0.092270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.067064 restraints weight = 91123.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068801 restraints weight = 47889.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069980 restraints weight = 31552.119| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23053 Z= 0.188 Angle : 0.659 14.192 31306 Z= 0.337 Chirality : 0.042 0.163 3583 Planarity : 0.005 0.055 4009 Dihedral : 6.263 84.302 3223 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.36 % Allowed : 16.63 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2908 helix: 1.55 (0.14), residues: 1430 sheet: -1.15 (0.28), residues: 330 loop : -2.61 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 49 HIS 0.006 0.001 HIS C 184 PHE 0.018 0.002 PHE B1316 TYR 0.032 0.002 TYR B 517 ARG 0.007 0.001 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 1140) hydrogen bonds : angle 4.25552 ( 3321) covalent geometry : bond 0.00427 (23053) covalent geometry : angle 0.65941 (31306) *********************** 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 200 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 144 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.5109 (tpt) cc_final: 0.4848 (tpp) REVERT: A 726 MET cc_start: 0.4705 (ppp) cc_final: 0.4444 (tmm) REVERT: A 734 MET cc_start: 0.8755 (tmm) cc_final: 0.8260 (tmm) REVERT: A 822 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: A 1193 GLU cc_start: 0.6093 (mp0) cc_final: 0.5645 (mp0) REVERT: B 517 TYR cc_start: 0.7352 (m-80) cc_final: 0.7095 (m-80) REVERT: B 541 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6343 (tt) REVERT: B 591 LEU cc_start: 0.8537 (mt) cc_final: 0.8045 (pp) REVERT: B 803 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8362 (pp) REVERT: B 886 MET cc_start: 0.8348 (tmm) cc_final: 0.8088 (tmm) REVERT: B 992 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8101 (t-90) REVERT: C 1 MET cc_start: 0.5383 (tpt) cc_final: 0.5099 (tpt) REVERT: C 136 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 143 SER cc_start: 0.8738 (t) cc_final: 0.8438 (p) outliers start: 56 outliers final: 37 residues processed: 188 average time/residue: 0.2948 time to fit residues: 94.6635 Evaluate side-chains 180 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 2.693 ------------------------------------------------------------------------------- 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 457 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR 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 712 THR Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1069 ASP 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 908 VAL Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1283 ASP 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 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 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 199 optimal weight: 0.0770 chunk 269 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.093556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068495 restraints weight = 90486.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070193 restraints weight = 47332.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.071516 restraints weight = 31029.129| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2462 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= 0.122 Angle : 0.624 14.364 31306 Z= 0.316 Chirality : 0.041 0.419 3583 Planarity : 0.004 0.054 4009 Dihedral : 6.151 85.894 3223 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.11 % Allowed : 17.81 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2908 helix: 1.73 (0.14), residues: 1423 sheet: -1.01 (0.29), residues: 325 loop : -2.55 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 307 HIS 0.015 0.001 HIS B1462 PHE 0.013 0.001 PHE A 377 TYR 0.030 0.001 TYR B 517 ARG 0.003 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1140) hydrogen bonds : angle 4.05412 ( 3321) covalent geometry : bond 0.00269 (23053) covalent geometry : angle 0.62373 (31306) *********************** 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 206 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8054 (tmm) cc_final: 0.7589 (ttt) REVERT: A 671 MET cc_start: 0.5124 (tpt) cc_final: 0.4911 (tpp) REVERT: A 681 MET cc_start: 0.5930 (tpp) cc_final: 0.5463 (tpp) REVERT: A 734 MET cc_start: 0.8770 (tmm) cc_final: 0.8384 (tmm) REVERT: A 822 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: A 1096 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: A 1193 GLU cc_start: 0.5894 (mp0) cc_final: 0.5507 (mp0) REVERT: B 517 TYR cc_start: 0.7368 (m-80) cc_final: 0.7088 (m-80) REVERT: B 541 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6314 (tt) REVERT: B 591 LEU cc_start: 0.8469 (mt) cc_final: 0.8005 (pp) REVERT: B 803 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8389 (pp) REVERT: B 992 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.8149 (t-90) REVERT: C 51 ASP cc_start: 0.7660 (p0) cc_final: 0.7223 (p0) REVERT: C 136 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 143 SER cc_start: 0.8724 (t) cc_final: 0.8412 (p) outliers start: 50 outliers final: 36 residues processed: 196 average time/residue: 0.3028 time to fit residues: 99.8545 Evaluate side-chains 186 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 132 LEU 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 587 THR 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 783 GLU 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 1069 ASP Chi-restraints excluded: chain A residue 1096 PHE 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 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 34 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 184 HIS 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 44 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 189 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 261 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN B 777 ASN ** B1151 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.090789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.065693 restraints weight = 90645.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067234 restraints weight = 48040.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068524 restraints weight = 32247.834| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23053 Z= 0.241 Angle : 0.708 14.715 31306 Z= 0.364 Chirality : 0.044 0.343 3583 Planarity : 0.005 0.055 4009 Dihedral : 6.437 86.533 3223 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.00 % Allowed : 17.43 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2908 helix: 1.39 (0.14), residues: 1437 sheet: -1.26 (0.26), residues: 356 loop : -2.64 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 49 HIS 0.008 0.001 HIS C 184 PHE 0.033 0.002 PHE B1479 TYR 0.028 0.002 TYR B 517 ARG 0.005 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1140) hydrogen bonds : angle 4.39633 ( 3321) covalent geometry : bond 0.00543 (23053) covalent geometry : angle 0.70751 (31306) *********************** 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 213 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 MET cc_start: 0.8801 (tmm) cc_final: 0.8310 (tmm) REVERT: A 822 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: A 1096 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: A 1193 GLU cc_start: 0.6182 (mp0) cc_final: 0.5793 (mp0) REVERT: B 517 TYR cc_start: 0.7290 (m-80) cc_final: 0.7047 (m-80) REVERT: B 591 LEU cc_start: 0.8635 (mt) cc_final: 0.8167 (pp) REVERT: B 803 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 886 MET cc_start: 0.8297 (tmm) cc_final: 0.8051 (tmm) REVERT: B 992 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8058 (t-90) REVERT: D 143 SER cc_start: 0.8776 (t) cc_final: 0.8498 (p) REVERT: D 175 PHE cc_start: 0.7627 (m-80) cc_final: 0.7422 (m-80) outliers start: 71 outliers final: 48 residues processed: 199 average time/residue: 0.2991 time to fit residues: 100.4313 Evaluate side-chains 188 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR 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 1059 VAL Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1222 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 713 VAL Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 992 HIS Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain B residue 1162 CYS Chi-restraints excluded: chain B residue 1283 ASP 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 201 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 255 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 HIS B1356 ASN B1462 HIS ** B1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.093445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068353 restraints weight = 90426.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.070055 restraints weight = 47176.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071352 restraints weight = 30997.228| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23053 Z= 0.121 Angle : 0.654 14.598 31306 Z= 0.329 Chirality : 0.042 0.389 3583 Planarity : 0.004 0.051 4009 Dihedral : 6.231 87.912 3223 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.11 % Allowed : 18.32 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2908 helix: 1.69 (0.14), residues: 1429 sheet: -1.07 (0.28), residues: 334 loop : -2.60 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 307 HIS 0.015 0.001 HIS B1462 PHE 0.014 0.001 PHE D 150 TYR 0.028 0.001 TYR B 517 ARG 0.004 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1140) hydrogen bonds : angle 4.04791 ( 3321) covalent geometry : bond 0.00263 (23053) covalent geometry : angle 0.65350 (31306) *********************** 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 195 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TYR cc_start: 0.7573 (m-80) cc_final: 0.7270 (m-80) REVERT: A 734 MET cc_start: 0.8769 (tmm) cc_final: 0.8430 (tmm) REVERT: A 822 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8628 (mp10) REVERT: A 1038 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 1096 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: A 1193 GLU cc_start: 0.5892 (mp0) cc_final: 0.5590 (mp0) REVERT: B 517 TYR cc_start: 0.7289 (m-80) cc_final: 0.7022 (m-80) REVERT: B 591 LEU cc_start: 0.8475 (mt) cc_final: 0.8012 (pp) REVERT: B 886 MET cc_start: 0.8257 (tmm) cc_final: 0.7999 (tmm) REVERT: B 992 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8159 (t-90) REVERT: C 136 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 143 SER cc_start: 0.8723 (t) cc_final: 0.8451 (p) outliers start: 50 outliers final: 37 residues processed: 183 average time/residue: 0.2952 time to fit residues: 91.6134 Evaluate side-chains 179 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU 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 793 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 913 THR 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 8 LEU 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 207 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 227 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 6 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 230 optimal weight: 0.0570 chunk 134 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 127 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** 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 = 0.3917 r_free = 0.3917 target = 0.093258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068169 restraints weight = 91180.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069975 restraints weight = 47708.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.071062 restraints weight = 31297.033| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23053 Z= 0.127 Angle : 0.644 15.188 31306 Z= 0.323 Chirality : 0.041 0.387 3583 Planarity : 0.005 0.111 4009 Dihedral : 6.128 88.592 3223 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.69 % Allowed : 18.83 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2908 helix: 1.75 (0.14), residues: 1433 sheet: -1.03 (0.28), residues: 325 loop : -2.54 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 307 HIS 0.015 0.001 HIS B1462 PHE 0.022 0.001 PHE B1316 TYR 0.027 0.001 TYR B 517 ARG 0.004 0.000 ARG A 630 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 1140) hydrogen bonds : angle 3.98469 ( 3321) covalent geometry : bond 0.00285 (23053) covalent geometry : angle 0.64356 (31306) ********************** 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 182 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TYR cc_start: 0.7574 (m-80) cc_final: 0.7299 (m-80) REVERT: A 681 MET cc_start: 0.5886 (tpp) cc_final: 0.5150 (tpp) REVERT: A 734 MET cc_start: 0.8803 (tmm) cc_final: 0.8468 (tmm) REVERT: A 822 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8630 (mp10) REVERT: A 1038 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 1096 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: A 1193 GLU cc_start: 0.6021 (mp0) cc_final: 0.5681 (mp0) REVERT: B 517 TYR cc_start: 0.7261 (m-80) cc_final: 0.6984 (m-80) REVERT: B 591 LEU cc_start: 0.8481 (mt) cc_final: 0.8008 (pp) REVERT: B 886 MET cc_start: 0.8300 (tmm) cc_final: 0.8031 (tmm) REVERT: C 136 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8103 (tm-30) REVERT: D 143 SER cc_start: 0.8631 (t) cc_final: 0.8343 (p) outliers start: 40 outliers final: 36 residues processed: 172 average time/residue: 0.2863 time to fit residues: 84.7545 Evaluate side-chains 177 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR 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 1059 VAL Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain B residue 657 MET Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 973 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 8 LEU 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 207 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 252 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.093048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067987 restraints weight = 90706.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069760 restraints weight = 47833.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070955 restraints weight = 31528.146| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23053 Z= 0.187 Angle : 0.782 59.186 31306 Z= 0.433 Chirality : 0.044 0.582 3583 Planarity : 0.005 0.108 4009 Dihedral : 6.146 88.579 3223 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.73 % Allowed : 18.87 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2908 helix: 1.73 (0.14), residues: 1432 sheet: -1.00 (0.28), residues: 335 loop : -2.56 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 307 HIS 0.011 0.001 HIS B1462 PHE 0.038 0.002 PHE C 9 TYR 0.026 0.001 TYR B 517 ARG 0.003 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1140) hydrogen bonds : angle 3.99857 ( 3321) covalent geometry : bond 0.00397 (23053) covalent geometry : angle 0.78170 (31306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7936.29 seconds wall clock time: 138 minutes 15.79 seconds (8295.79 seconds total)