Starting phenix.real_space_refine on Sat Mar 7 04:44:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6puo_20478/03_2026/6puo_20478.cif Found real_map, /net/cci-nas-00/data/ceres_data/6puo_20478/03_2026/6puo_20478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6puo_20478/03_2026/6puo_20478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6puo_20478/03_2026/6puo_20478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6puo_20478/03_2026/6puo_20478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6puo_20478/03_2026/6puo_20478.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 24384 2.51 5 N 6680 2.21 5 O 6592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37804 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 9451 Classifications: {'peptide': 1302} Incomplete info: {'truncation_to_alanine': 291} Link IDs: {'PTRANS': 62, 'TRANS': 1239} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1095 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 21, 'GLU:plan': 48, 'PHE:plan': 11, 'ASP:plan': 33, 'HIS:plan': 10, 'TRP:plan': 5, 'ARG:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 711 Restraints were copied for chains: B, C, D Time building chain proxies: 11.79, per 1000 atoms: 0.31 Number of scatterers: 37804 At special positions: 0 Unit cell: (175.062, 175.062, 166.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 6592 8.00 N 6680 7.00 C 24384 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: 3.16 Conformation dependent library (CDL) restraints added in 1.8 seconds 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9832 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 32 sheets defined 54.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.518A pdb=" N VAL A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.748A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.711A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.859A pdb=" N GLY A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 4.143A pdb=" N LEU A 236 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.702A pdb=" N GLY A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.166A pdb=" N ARG A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.853A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.718A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 398 through 412 removed outlier: 4.175A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 443 Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.668A pdb=" N ASP A 453 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.546A pdb=" N THR A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.655A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.518A pdb=" N LEU A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.706A pdb=" N SER A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.819A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 4.221A pdb=" N ASP A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 668 through 697 removed outlier: 3.661A pdb=" N GLU A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.500A pdb=" N THR A 706 " --> pdb=" O LYS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 removed outlier: 3.858A pdb=" N ALA A 721 " --> pdb=" O CYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.774A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.842A pdb=" N ALA A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 819 Processing helix chain 'A' and resid 826 through 848 removed outlier: 3.530A pdb=" N CYS A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.539A pdb=" N THR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 908 Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.734A pdb=" N PHE A 914 " --> pdb=" O MET A 911 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 915 " --> pdb=" O HIS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 956 removed outlier: 5.069A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 980 removed outlier: 3.535A pdb=" N GLY A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1036 Processing helix chain 'A' and resid 1038 through 1056 removed outlier: 3.940A pdb=" N VAL A1055 " --> pdb=" O THR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1077 removed outlier: 3.872A pdb=" N ILE A1062 " --> pdb=" O HIS A1058 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N HIS A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A1069 " --> pdb=" O PHE A1065 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A1070 " --> pdb=" O GLN A1066 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1098 Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 3.837A pdb=" N ALA A1120 " --> pdb=" O ASN A1116 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A1142 " --> pdb=" O PHE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1165 removed outlier: 3.895A pdb=" N ASP A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A1157 " --> pdb=" O ASN A1153 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1282 removed outlier: 4.072A pdb=" N ASP A1282 " --> pdb=" O GLU A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1279 through 1282' Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 4.336A pdb=" N ASP A1291 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1404 Processing helix chain 'A' and resid 1409 through 1419 removed outlier: 3.877A pdb=" N SER A1413 " --> pdb=" O GLU A1409 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A1414 " --> pdb=" O HIS A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1463 removed outlier: 3.639A pdb=" N ARG A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1496 removed outlier: 3.851A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.519A pdb=" N VAL B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.748A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.711A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.860A pdb=" N GLY B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.144A pdb=" N LEU B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.702A pdb=" N GLY B 252 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.167A pdb=" N ARG B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.853A pdb=" N LEU B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.718A pdb=" N ILE B 363 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 398 through 412 removed outlier: 4.175A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.667A pdb=" N ASP B 453 " --> pdb=" O HIS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.546A pdb=" N THR B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 506 removed outlier: 3.655A pdb=" N VAL B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.518A pdb=" N LEU B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.706A pdb=" N SER B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 557 through 570 removed outlier: 3.819A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 4.221A pdb=" N ASP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 647 through 663 Processing helix chain 'B' and resid 668 through 697 removed outlier: 3.661A pdb=" N GLU B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 Processing helix chain 'B' and resid 717 through 724 removed outlier: 3.858A pdb=" N ALA B 721 " --> pdb=" O CYS B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 733 through 745 Processing helix chain 'B' and resid 752 through 762 removed outlier: 3.775A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.842A pdb=" N ALA B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 819 Processing helix chain 'B' and resid 826 through 848 removed outlier: 3.530A pdb=" N CYS B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 865 Processing helix chain 'B' and resid 866 through 888 removed outlier: 3.539A pdb=" N THR B 884 " --> pdb=" O VAL B 880 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 888 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 908 Processing helix chain 'B' and resid 909 through 916 removed outlier: 3.734A pdb=" N PHE B 914 " --> pdb=" O MET B 911 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 915 " --> pdb=" O HIS B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 956 removed outlier: 5.069A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 980 removed outlier: 3.536A pdb=" N GLY B 980 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1036 Processing helix chain 'B' and resid 1038 through 1056 removed outlier: 3.941A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1077 removed outlier: 3.872A pdb=" N ILE B1062 " --> pdb=" O HIS B1058 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N HIS B1068 " --> pdb=" O LYS B1064 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP B1069 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B1074 " --> pdb=" O LEU B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1098 Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 3.837A pdb=" N ALA B1120 " --> pdb=" O ASN B1116 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B1142 " --> pdb=" O PHE B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1165 removed outlier: 3.895A pdb=" N ASP B1156 " --> pdb=" O SER B1152 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B1157 " --> pdb=" O ASN B1153 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1282 removed outlier: 4.072A pdb=" N ASP B1282 " --> pdb=" O GLU B1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1279 through 1282' Processing helix chain 'B' and resid 1288 through 1292 removed outlier: 4.336A pdb=" N ASP B1291 " --> pdb=" O PRO B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1397 through 1404 Processing helix chain 'B' and resid 1409 through 1419 removed outlier: 3.877A pdb=" N SER B1413 " --> pdb=" O GLU B1409 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B1414 " --> pdb=" O HIS B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1463 removed outlier: 3.639A pdb=" N ARG B1459 " --> pdb=" O VAL B1455 " (cutoff:3.500A) Processing helix chain 'B' and resid 1487 through 1496 removed outlier: 3.851A pdb=" N LEU B1491 " --> pdb=" O ASN B1487 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.518A pdb=" N VAL C 119 " --> pdb=" O PRO C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.748A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 202 removed outlier: 3.711A pdb=" N GLY C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.859A pdb=" N GLY C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.143A pdb=" N LEU C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.702A pdb=" N GLY C 252 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 310 removed outlier: 4.165A pdb=" N ARG C 304 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 346 removed outlier: 3.853A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 removed outlier: 3.718A pdb=" N ILE C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 387 Processing helix chain 'C' and resid 398 through 412 removed outlier: 4.175A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 443 Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.668A pdb=" N ASP C 453 " --> pdb=" O HIS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 484 through 494 removed outlier: 3.546A pdb=" N THR C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 506 removed outlier: 3.655A pdb=" N VAL C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.518A pdb=" N LEU C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 542 removed outlier: 3.706A pdb=" N SER C 534 " --> pdb=" O CYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 557 through 570 removed outlier: 3.819A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 568 " --> pdb=" O VAL C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 631 removed outlier: 4.221A pdb=" N ASP C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 Processing helix chain 'C' and resid 643 through 645 No H-bonds generated for 'chain 'C' and resid 643 through 645' Processing helix chain 'C' and resid 647 through 663 Processing helix chain 'C' and resid 668 through 697 removed outlier: 3.661A pdb=" N GLU C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 697 " --> pdb=" O CYS C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.500A pdb=" N THR C 706 " --> pdb=" O LYS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 724 removed outlier: 3.858A pdb=" N ALA C 721 " --> pdb=" O CYS C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 731 Processing helix chain 'C' and resid 733 through 745 Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.774A pdb=" N VAL C 756 " --> pdb=" O GLY C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 783 through 794 removed outlier: 3.842A pdb=" N ALA C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 819 Processing helix chain 'C' and resid 826 through 848 removed outlier: 3.530A pdb=" N CYS C 830 " --> pdb=" O SER C 826 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 847 " --> pdb=" O GLU C 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 865 Processing helix chain 'C' and resid 866 through 888 removed outlier: 3.539A pdb=" N THR C 884 " --> pdb=" O VAL C 880 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 888 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 908 Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.734A pdb=" N PHE C 914 " --> pdb=" O MET C 911 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 915 " --> pdb=" O HIS C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 956 removed outlier: 5.069A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 956 " --> pdb=" O LYS C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 980 removed outlier: 3.535A pdb=" N GLY C 980 " --> pdb=" O LEU C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1036 Processing helix chain 'C' and resid 1038 through 1056 removed outlier: 3.940A pdb=" N VAL C1055 " --> pdb=" O THR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1077 removed outlier: 3.872A pdb=" N ILE C1062 " --> pdb=" O HIS C1058 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N HIS C1068 " --> pdb=" O LYS C1064 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP C1069 " --> pdb=" O PHE C1065 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C1074 " --> pdb=" O LEU C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1098 Processing helix chain 'C' and resid 1114 through 1142 removed outlier: 3.837A pdb=" N ALA C1120 " --> pdb=" O ASN C1116 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C1142 " --> pdb=" O PHE C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1165 removed outlier: 3.895A pdb=" N ASP C1156 " --> pdb=" O SER C1152 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA C1157 " --> pdb=" O ASN C1153 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP C1165 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1282 removed outlier: 4.072A pdb=" N ASP C1282 " --> pdb=" O GLU C1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1279 through 1282' Processing helix chain 'C' and resid 1288 through 1292 removed outlier: 4.336A pdb=" N ASP C1291 " --> pdb=" O PRO C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1397 through 1404 Processing helix chain 'C' and resid 1409 through 1419 removed outlier: 3.877A pdb=" N SER C1413 " --> pdb=" O GLU C1409 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C1414 " --> pdb=" O HIS C1410 " (cutoff:3.500A) Processing helix chain 'C' and resid 1455 through 1463 removed outlier: 3.639A pdb=" N ARG C1459 " --> pdb=" O VAL C1455 " (cutoff:3.500A) Processing helix chain 'C' and resid 1487 through 1496 removed outlier: 3.851A pdb=" N LEU C1491 " --> pdb=" O ASN C1487 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.518A pdb=" N VAL D 119 " --> pdb=" O PRO D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.748A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.711A pdb=" N GLY D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.859A pdb=" N GLY D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 4.143A pdb=" N LEU D 236 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.702A pdb=" N GLY D 252 " --> pdb=" O ARG D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 4.166A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 346 removed outlier: 3.853A pdb=" N LEU D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 3.718A pdb=" N ILE D 363 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 398 through 412 removed outlier: 4.176A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 462 removed outlier: 3.667A pdb=" N ASP D 453 " --> pdb=" O HIS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 484 through 494 removed outlier: 3.546A pdb=" N THR D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 494 " --> pdb=" O ALA D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 506 removed outlier: 3.656A pdb=" N VAL D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 515 through 523 removed outlier: 3.518A pdb=" N LEU D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 542 removed outlier: 3.706A pdb=" N SER D 534 " --> pdb=" O CYS D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.819A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 568 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 4.221A pdb=" N ASP D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 642 Processing helix chain 'D' and resid 643 through 645 No H-bonds generated for 'chain 'D' and resid 643 through 645' Processing helix chain 'D' and resid 647 through 663 Processing helix chain 'D' and resid 668 through 697 removed outlier: 3.660A pdb=" N GLU D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 697 " --> pdb=" O CYS D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.500A pdb=" N THR D 706 " --> pdb=" O LYS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 724 removed outlier: 3.858A pdb=" N ALA D 721 " --> pdb=" O CYS D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 731 Processing helix chain 'D' and resid 733 through 745 Processing helix chain 'D' and resid 752 through 762 removed outlier: 3.774A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 781 Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.842A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 819 Processing helix chain 'D' and resid 826 through 848 removed outlier: 3.530A pdb=" N CYS D 830 " --> pdb=" O SER D 826 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 847 " --> pdb=" O GLU D 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 865 Processing helix chain 'D' and resid 866 through 888 removed outlier: 3.539A pdb=" N THR D 884 " --> pdb=" O VAL D 880 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE D 888 " --> pdb=" O THR D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 908 Processing helix chain 'D' and resid 909 through 916 removed outlier: 3.734A pdb=" N PHE D 914 " --> pdb=" O MET D 911 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 915 " --> pdb=" O HIS D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 956 removed outlier: 5.069A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 956 " --> pdb=" O LYS D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 980 removed outlier: 3.535A pdb=" N GLY D 980 " --> pdb=" O LEU D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1036 Processing helix chain 'D' and resid 1038 through 1056 removed outlier: 3.940A pdb=" N VAL D1055 " --> pdb=" O THR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1077 removed outlier: 3.872A pdb=" N ILE D1062 " --> pdb=" O HIS D1058 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N HIS D1068 " --> pdb=" O LYS D1064 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASP D1069 " --> pdb=" O PHE D1065 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D1070 " --> pdb=" O GLN D1066 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D1074 " --> pdb=" O LEU D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1098 Processing helix chain 'D' and resid 1114 through 1142 removed outlier: 3.837A pdb=" N ALA D1120 " --> pdb=" O ASN D1116 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN D1142 " --> pdb=" O PHE D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1165 removed outlier: 3.895A pdb=" N ASP D1156 " --> pdb=" O SER D1152 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA D1157 " --> pdb=" O ASN D1153 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET D1158 " --> pdb=" O LYS D1154 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP D1165 " --> pdb=" O LEU D1161 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1282 removed outlier: 4.072A pdb=" N ASP D1282 " --> pdb=" O GLU D1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1279 through 1282' Processing helix chain 'D' and resid 1288 through 1292 removed outlier: 4.335A pdb=" N ASP D1291 " --> pdb=" O PRO D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1404 Processing helix chain 'D' and resid 1409 through 1419 removed outlier: 3.877A pdb=" N SER D1413 " --> pdb=" O GLU D1409 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D1414 " --> pdb=" O HIS D1410 " (cutoff:3.500A) Processing helix chain 'D' and resid 1455 through 1463 removed outlier: 3.640A pdb=" N ARG D1459 " --> pdb=" O VAL D1455 " (cutoff:3.500A) Processing helix chain 'D' and resid 1487 through 1496 removed outlier: 3.851A pdb=" N LEU D1491 " --> pdb=" O ASN D1487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 7.975A pdb=" N TYR A 264 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 131 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS A 141 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU A 286 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 143 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 238 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 285 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY A 240 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 287 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 242 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA A 203 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE A 239 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 205 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 241 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 207 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N THR A 243 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY A 208 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 328 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS A 350 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316 Processing sheet with id=AA4, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.862A pdb=" N THR A 715 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1275 through 1277 removed outlier: 3.589A pdb=" N ARG A1336 " --> pdb=" O TYR A1276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AA7, first strand: chain 'A' and resid 1385 through 1386 removed outlier: 3.759A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL A1377 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP A1355 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE A1440 " --> pdb=" O TYR A1428 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A1428 " --> pdb=" O ILE A1440 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR A1442 " --> pdb=" O LYS A1426 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS A1426 " --> pdb=" O THR A1442 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A1444 " --> pdb=" O VAL A1424 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A1422 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1385 through 1386 Processing sheet with id=AA9, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 264 removed outlier: 7.974A pdb=" N TYR B 264 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 131 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 141 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU B 286 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 143 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR B 238 " --> pdb=" O HIS B 283 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE B 285 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY B 240 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B 287 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 242 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA B 203 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE B 239 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 205 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL B 241 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR B 207 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N THR B 243 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY B 208 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 328 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS B 350 " --> pdb=" O THR B 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AB3, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.862A pdb=" N THR B 715 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1275 through 1277 removed outlier: 3.590A pdb=" N ARG B1336 " --> pdb=" O TYR B1276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1319 through 1320 Processing sheet with id=AB6, first strand: chain 'B' and resid 1385 through 1386 removed outlier: 3.759A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL B1377 " --> pdb=" O PRO B1350 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP B1355 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE B1440 " --> pdb=" O TYR B1428 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR B1428 " --> pdb=" O ILE B1440 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B1442 " --> pdb=" O LYS B1426 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS B1426 " --> pdb=" O THR B1442 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B1444 " --> pdb=" O VAL B1424 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B1422 " --> pdb=" O SER B1446 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1385 through 1386 Processing sheet with id=AB8, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AB9, first strand: chain 'C' and resid 263 through 264 removed outlier: 7.975A pdb=" N TYR C 264 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 131 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS C 141 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU C 286 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 143 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 238 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE C 285 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY C 240 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C 287 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 242 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE C 239 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C 205 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL C 241 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C 207 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N THR C 243 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLY C 208 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 328 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS C 350 " --> pdb=" O THR C 417 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 313 through 316 Processing sheet with id=AC2, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.862A pdb=" N THR C 715 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1275 through 1277 removed outlier: 3.589A pdb=" N ARG C1336 " --> pdb=" O TYR C1276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1319 through 1320 Processing sheet with id=AC5, first strand: chain 'C' and resid 1385 through 1386 removed outlier: 3.759A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL C1377 " --> pdb=" O PRO C1350 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP C1355 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE C1440 " --> pdb=" O TYR C1428 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR C1428 " --> pdb=" O ILE C1440 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C1442 " --> pdb=" O LYS C1426 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C1426 " --> pdb=" O THR C1442 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA C1444 " --> pdb=" O VAL C1424 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C1422 " --> pdb=" O SER C1446 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1385 through 1386 Processing sheet with id=AC7, first strand: chain 'D' and resid 68 through 71 Processing sheet with id=AC8, first strand: chain 'D' and resid 263 through 264 removed outlier: 7.974A pdb=" N TYR D 264 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL D 131 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS D 141 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU D 286 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 143 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR D 238 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE D 285 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY D 240 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL D 287 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 242 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA D 203 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE D 239 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 205 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL D 241 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR D 207 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N THR D 243 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY D 208 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 328 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS D 350 " --> pdb=" O THR D 417 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 313 through 316 Processing sheet with id=AD1, first strand: chain 'D' and resid 708 through 709 removed outlier: 3.862A pdb=" N THR D 715 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1275 through 1277 removed outlier: 3.589A pdb=" N ARG D1336 " --> pdb=" O TYR D1276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1319 through 1320 Processing sheet with id=AD4, first strand: chain 'D' and resid 1385 through 1386 removed outlier: 3.760A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL D1377 " --> pdb=" O PRO D1350 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP D1355 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE D1440 " --> pdb=" O TYR D1428 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR D1428 " --> pdb=" O ILE D1440 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR D1442 " --> pdb=" O LYS D1426 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS D1426 " --> pdb=" O THR D1442 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA D1444 " --> pdb=" O VAL D1424 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET D1422 " --> pdb=" O SER D1446 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1385 through 1386 1942 hydrogen bonds defined for protein. 5655 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: 8.46 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12248 1.34 - 1.46: 7258 1.46 - 1.57: 18970 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 38700 Sorted by residual: bond pdb=" C TRP C 479 " pdb=" N LYS C 480 " ideal model delta sigma weight residual 1.333 1.233 0.100 2.74e-02 1.33e+03 1.32e+01 bond pdb=" C TRP D 479 " pdb=" N LYS D 480 " ideal model delta sigma weight residual 1.333 1.233 0.100 2.74e-02 1.33e+03 1.32e+01 bond pdb=" C TRP A 479 " pdb=" N LYS A 480 " ideal model delta sigma weight residual 1.333 1.233 0.100 2.74e-02 1.33e+03 1.32e+01 bond pdb=" C TRP B 479 " pdb=" N LYS B 480 " ideal model delta sigma weight residual 1.333 1.233 0.100 2.74e-02 1.33e+03 1.32e+01 bond pdb=" N ILE C 771 " pdb=" CA ILE C 771 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.15e-02 7.56e+03 1.24e+01 ... (remaining 38695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 50198 1.78 - 3.56: 2302 3.56 - 5.34: 256 5.34 - 7.12: 88 7.12 - 8.91: 68 Bond angle restraints: 52912 Sorted by residual: angle pdb=" C TYR D1301 " pdb=" N ASN D1302 " pdb=" CA ASN D1302 " ideal model delta sigma weight residual 122.46 130.05 -7.59 1.41e+00 5.03e-01 2.90e+01 angle pdb=" C TYR C1301 " pdb=" N ASN C1302 " pdb=" CA ASN C1302 " ideal model delta sigma weight residual 122.46 130.05 -7.59 1.41e+00 5.03e-01 2.90e+01 angle pdb=" C TYR A1301 " pdb=" N ASN A1302 " pdb=" CA ASN A1302 " ideal model delta sigma weight residual 122.46 130.05 -7.59 1.41e+00 5.03e-01 2.90e+01 angle pdb=" C TYR B1301 " pdb=" N ASN B1302 " pdb=" CA ASN B1302 " ideal model delta sigma weight residual 122.46 130.02 -7.56 1.41e+00 5.03e-01 2.87e+01 angle pdb=" N ILE C1270 " pdb=" CA ILE C1270 " pdb=" C ILE C1270 " ideal model delta sigma weight residual 112.29 107.71 4.58 9.40e-01 1.13e+00 2.38e+01 ... (remaining 52907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 20550 15.99 - 31.99: 1748 31.99 - 47.98: 390 47.98 - 63.98: 40 63.98 - 79.97: 60 Dihedral angle restraints: 22788 sinusoidal: 7652 harmonic: 15136 Sorted by residual: dihedral pdb=" CA ILE D1038 " pdb=" C ILE D1038 " pdb=" N LEU D1039 " pdb=" CA LEU D1039 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE C1038 " pdb=" C ILE C1038 " pdb=" N LEU C1039 " pdb=" CA LEU C1039 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE A1038 " pdb=" C ILE A1038 " pdb=" N LEU A1039 " pdb=" CA LEU A1039 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 22785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4333 0.049 - 0.097: 1424 0.097 - 0.146: 371 0.146 - 0.194: 60 0.194 - 0.243: 20 Chirality restraints: 6208 Sorted by residual: chirality pdb=" CB VAL B 366 " pdb=" CA VAL B 366 " pdb=" CG1 VAL B 366 " pdb=" CG2 VAL B 366 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL C 366 " pdb=" CA VAL C 366 " pdb=" CG1 VAL C 366 " pdb=" CG2 VAL C 366 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL A 366 " pdb=" CA VAL A 366 " pdb=" CG1 VAL A 366 " pdb=" CG2 VAL A 366 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 6205 not shown) Planarity restraints: 6784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1082 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO B1083 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B1083 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B1083 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C1082 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO C1083 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C1083 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1083 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D1082 " -0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO D1083 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D1083 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D1083 " -0.038 5.00e-02 4.00e+02 ... (remaining 6781 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 12415 2.82 - 3.34: 35786 3.34 - 3.86: 61278 3.86 - 4.38: 64812 4.38 - 4.90: 111157 Nonbonded interactions: 285448 Sorted by model distance: nonbonded pdb=" OG1 THR D1347 " pdb=" O GLY D1390 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR C1347 " pdb=" O GLY C1390 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR A1347 " pdb=" O GLY A1390 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR B1347 " pdb=" O GLY B1390 " model vdw 2.305 3.040 nonbonded pdb=" O TRP B 835 " pdb=" OG SER B 838 " model vdw 2.320 3.040 ... (remaining 285443 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.690 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 0.100 38700 Z= 0.356 Angle : 0.905 8.906 52912 Z= 0.514 Chirality : 0.052 0.243 6208 Planarity : 0.007 0.066 6784 Dihedral : 13.532 79.971 12956 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.35 % Favored : 92.49 % Rotamer: Outliers : 0.35 % Allowed : 8.30 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.09), residues: 5168 helix: -1.81 (0.08), residues: 2556 sheet: -2.06 (0.23), residues: 424 loop : -2.88 (0.11), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1105 TYR 0.020 0.002 TYR B 682 PHE 0.016 0.002 PHE B 906 TRP 0.017 0.002 TRP C 743 HIS 0.008 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00739 (38700) covalent geometry : angle 0.90477 (52912) hydrogen bonds : bond 0.16843 ( 1934) hydrogen bonds : angle 6.04158 ( 5655) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 243 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9133 (mtm) cc_final: 0.8911 (mtp) REVERT: A 680 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 122 MET cc_start: 0.8843 (mtm) cc_final: 0.8637 (mpp) REVERT: B 158 MET cc_start: 0.9126 (mtm) cc_final: 0.8909 (mtp) REVERT: B 680 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 158 MET cc_start: 0.9133 (mtm) cc_final: 0.8911 (mtp) REVERT: C 680 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7762 (tm-30) REVERT: D 122 MET cc_start: 0.8855 (mtm) cc_final: 0.8636 (mpp) REVERT: D 158 MET cc_start: 0.9119 (mtm) cc_final: 0.8917 (mtp) REVERT: D 680 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7768 (tm-30) REVERT: D 857 MET cc_start: 0.8085 (tmm) cc_final: 0.7347 (tmm) REVERT: D 1158 MET cc_start: 0.9046 (mtp) cc_final: 0.8800 (mtt) outliers start: 12 outliers final: 8 residues processed: 255 average time/residue: 0.2065 time to fit residues: 91.9596 Evaluate side-chains 184 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1262 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 516 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 281 HIS A 283 HIS A 292 HIS ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 506 ASN A 560 HIS A 732 HIS A 912 HIS A1089 HIS A1139 GLN A1437 ASN B 120 GLN B 281 HIS B 283 HIS B 292 HIS ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 506 ASN B 560 HIS B 732 HIS B 912 HIS B1089 HIS B1139 GLN B1437 ASN C 120 GLN C 281 HIS C 283 HIS C 292 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 506 ASN C 560 HIS C 732 HIS C 912 HIS C1089 HIS C1139 GLN C1437 ASN D 120 GLN D 281 HIS D 283 HIS D 292 HIS ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN D 506 ASN D 560 HIS D 732 HIS D 912 HIS D1089 HIS D1139 GLN D1437 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.079310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053039 restraints weight = 139760.588| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.46 r_work: 0.2822 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38700 Z= 0.129 Angle : 0.549 5.476 52912 Z= 0.287 Chirality : 0.039 0.200 6208 Planarity : 0.005 0.056 6784 Dihedral : 5.345 55.630 5520 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 1.70 % Allowed : 11.35 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.11), residues: 5168 helix: 0.22 (0.10), residues: 2632 sheet: -2.08 (0.22), residues: 428 loop : -2.51 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1357 TYR 0.014 0.001 TYR A 682 PHE 0.009 0.001 PHE B 799 TRP 0.012 0.001 TRP C 743 HIS 0.004 0.000 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00284 (38700) covalent geometry : angle 0.54923 (52912) hydrogen bonds : bond 0.04672 ( 1934) hydrogen bonds : angle 4.13442 ( 5655) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 1.434 Fit side-chains REVERT: B 182 MET cc_start: 0.8556 (ptp) cc_final: 0.8290 (ptm) REVERT: D 182 MET cc_start: 0.8555 (ptp) cc_final: 0.8294 (ptm) outliers start: 58 outliers final: 27 residues processed: 239 average time/residue: 0.1947 time to fit residues: 83.0260 Evaluate side-chains 199 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 759 CYS Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 759 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 759 CYS Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 231 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 312 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 280 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 822 GLN A1049 ASN A1450 GLN A1488 HIS ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 822 GLN B1450 GLN B1488 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 ASN C 822 GLN C1450 GLN C1488 HIS ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 ASN D 822 GLN D1049 ASN D1450 GLN D1488 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.077642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050881 restraints weight = 140486.859| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.46 r_work: 0.2755 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 38700 Z= 0.243 Angle : 0.614 7.497 52912 Z= 0.320 Chirality : 0.042 0.182 6208 Planarity : 0.005 0.051 6784 Dihedral : 5.010 56.485 5514 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.97 % Favored : 92.96 % Rotamer: Outliers : 1.73 % Allowed : 12.84 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.12), residues: 5168 helix: 0.95 (0.10), residues: 2612 sheet: -2.33 (0.21), residues: 440 loop : -2.25 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1105 TYR 0.017 0.001 TYR B 682 PHE 0.014 0.001 PHE B 799 TRP 0.014 0.001 TRP D 743 HIS 0.007 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00567 (38700) covalent geometry : angle 0.61423 (52912) hydrogen bonds : bond 0.05572 ( 1934) hydrogen bonds : angle 4.09735 ( 5655) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 MET cc_start: 0.8688 (ptp) cc_final: 0.8391 (ptm) outliers start: 59 outliers final: 39 residues processed: 215 average time/residue: 0.1770 time to fit residues: 69.6974 Evaluate side-chains 194 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 822 GLN Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 945 VAL Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 180 optimal weight: 4.9990 chunk 382 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 368 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 443 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 350 optimal weight: 5.9990 chunk 412 optimal weight: 8.9990 chunk 283 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 HIS ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.078886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052292 restraints weight = 139141.842| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.43 r_work: 0.2794 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38700 Z= 0.138 Angle : 0.530 9.587 52912 Z= 0.275 Chirality : 0.040 0.194 6208 Planarity : 0.004 0.048 6784 Dihedral : 4.678 39.731 5512 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 1.90 % Allowed : 13.83 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 5168 helix: 1.37 (0.10), residues: 2616 sheet: -2.22 (0.21), residues: 440 loop : -2.11 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 412 TYR 0.013 0.001 TYR A 682 PHE 0.008 0.001 PHE D 799 TRP 0.010 0.001 TRP B 743 HIS 0.005 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00318 (38700) covalent geometry : angle 0.53040 (52912) hydrogen bonds : bond 0.04502 ( 1934) hydrogen bonds : angle 3.81760 ( 5655) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 1.441 Fit side-chains REVERT: A 948 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7846 (t80) REVERT: B 182 MET cc_start: 0.8624 (ptp) cc_final: 0.8307 (ptm) REVERT: B 948 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7897 (t80) REVERT: C 948 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7895 (t80) outliers start: 65 outliers final: 30 residues processed: 219 average time/residue: 0.1836 time to fit residues: 73.7352 Evaluate side-chains 191 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 CYS Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 759 CYS Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 759 CYS Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 945 VAL Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 88 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 371 optimal weight: 30.0000 chunk 469 optimal weight: 20.0000 chunk 259 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.077561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050786 restraints weight = 140106.410| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.39 r_work: 0.2748 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 38700 Z= 0.244 Angle : 0.605 11.064 52912 Z= 0.311 Chirality : 0.042 0.182 6208 Planarity : 0.004 0.046 6784 Dihedral : 4.728 40.416 5512 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.12 % Favored : 92.80 % Rotamer: Outliers : 2.75 % Allowed : 13.60 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.12), residues: 5168 helix: 1.52 (0.10), residues: 2612 sheet: -2.29 (0.20), residues: 440 loop : -2.00 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.018 0.001 TYR D 682 PHE 0.014 0.001 PHE B 260 TRP 0.012 0.001 TRP C 743 HIS 0.006 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00574 (38700) covalent geometry : angle 0.60515 (52912) hydrogen bonds : bond 0.05418 ( 1934) hydrogen bonds : angle 3.99665 ( 5655) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 169 time to evaluate : 1.641 Fit side-chains REVERT: A 887 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8231 (mm) REVERT: A 941 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8987 (mm) REVERT: A 948 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7853 (t80) REVERT: A 1158 MET cc_start: 0.9297 (ttp) cc_final: 0.8719 (ttm) REVERT: B 887 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8231 (mm) REVERT: B 941 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9008 (mm) REVERT: B 948 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7860 (t80) REVERT: B 1158 MET cc_start: 0.9082 (mtt) cc_final: 0.8643 (mtp) REVERT: C 887 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8231 (mm) REVERT: C 941 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9009 (mm) REVERT: C 948 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7882 (t80) REVERT: D 887 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8227 (mm) REVERT: D 941 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8996 (mm) REVERT: D 1158 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8845 (ttm) outliers start: 94 outliers final: 52 residues processed: 248 average time/residue: 0.1831 time to fit residues: 83.1780 Evaluate side-chains 227 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 944 TRP Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 944 TRP Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 759 CYS Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 944 TRP Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 759 CYS Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 944 TRP Chi-restraints excluded: chain D residue 945 VAL Chi-restraints excluded: chain D residue 1158 MET Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1377 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 234 optimal weight: 5.9990 chunk 396 optimal weight: 0.5980 chunk 365 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 500 optimal weight: 40.0000 chunk 445 optimal weight: 0.8980 chunk 442 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052558 restraints weight = 138655.400| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.43 r_work: 0.2796 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38700 Z= 0.122 Angle : 0.534 12.716 52912 Z= 0.268 Chirality : 0.039 0.163 6208 Planarity : 0.004 0.047 6784 Dihedral : 4.485 41.296 5512 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 1.75 % Allowed : 15.56 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.12), residues: 5168 helix: 1.70 (0.10), residues: 2644 sheet: -2.12 (0.21), residues: 436 loop : -1.90 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 412 TYR 0.013 0.001 TYR B 682 PHE 0.010 0.001 PHE D1048 TRP 0.009 0.001 TRP B 743 HIS 0.005 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00280 (38700) covalent geometry : angle 0.53350 (52912) hydrogen bonds : bond 0.04174 ( 1934) hydrogen bonds : angle 3.72810 ( 5655) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 1.827 Fit side-chains REVERT: A 948 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7804 (t80) REVERT: A 1158 MET cc_start: 0.9291 (ttp) cc_final: 0.8815 (ttm) REVERT: B 948 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7811 (t80) REVERT: B 1158 MET cc_start: 0.9066 (mtt) cc_final: 0.8763 (mtp) REVERT: C 948 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7826 (t80) outliers start: 60 outliers final: 38 residues processed: 232 average time/residue: 0.1877 time to fit residues: 79.9871 Evaluate side-chains 205 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 944 TRP Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 CYS Chi-restraints excluded: chain B residue 944 TRP Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 759 CYS Chi-restraints excluded: chain C residue 944 TRP Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 759 CYS Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 944 TRP Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1377 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 192 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 413 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 283 optimal weight: 9.9990 chunk 443 optimal weight: 4.9990 chunk 517 optimal weight: 5.9990 chunk 303 optimal weight: 0.0870 chunk 134 optimal weight: 0.0030 chunk 6 optimal weight: 0.9980 overall best weight: 2.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.079231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052647 restraints weight = 138819.965| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.44 r_work: 0.2772 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38700 Z= 0.126 Angle : 0.534 12.653 52912 Z= 0.266 Chirality : 0.039 0.157 6208 Planarity : 0.004 0.046 6784 Dihedral : 4.324 41.577 5512 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.40 % Rotamer: Outliers : 2.28 % Allowed : 15.91 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5168 helix: 1.81 (0.10), residues: 2660 sheet: -1.91 (0.21), residues: 436 loop : -1.84 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 412 TYR 0.013 0.001 TYR B 682 PHE 0.012 0.001 PHE A1048 TRP 0.010 0.001 TRP C 743 HIS 0.005 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00292 (38700) covalent geometry : angle 0.53366 (52912) hydrogen bonds : bond 0.04067 ( 1934) hydrogen bonds : angle 3.64402 ( 5655) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 171 time to evaluate : 1.546 Fit side-chains REVERT: A 887 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8162 (mm) REVERT: A 941 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8949 (mm) REVERT: A 948 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 1158 MET cc_start: 0.9198 (ttp) cc_final: 0.8989 (ttp) REVERT: B 887 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8164 (mm) REVERT: B 941 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8945 (mm) REVERT: B 948 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7794 (t80) REVERT: C 887 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8162 (mm) REVERT: C 941 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8946 (mm) REVERT: D 887 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8162 (mm) REVERT: D 941 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8952 (mm) REVERT: D 948 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7788 (t80) outliers start: 78 outliers final: 46 residues processed: 242 average time/residue: 0.2146 time to fit residues: 92.5884 Evaluate side-chains 215 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 944 TRP Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 944 TRP Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 944 TRP Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 944 TRP Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 73 optimal weight: 1.9990 chunk 448 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 320 optimal weight: 0.3980 chunk 416 optimal weight: 0.3980 chunk 464 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 410 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** 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 = 0.3648 r_free = 0.3648 target = 0.080455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054107 restraints weight = 138283.482| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.41 r_work: 0.2815 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38700 Z= 0.093 Angle : 0.521 13.052 52912 Z= 0.254 Chirality : 0.038 0.172 6208 Planarity : 0.004 0.046 6784 Dihedral : 4.130 42.024 5512 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 1.84 % Allowed : 16.49 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 5168 helix: 1.90 (0.11), residues: 2672 sheet: -1.79 (0.21), residues: 444 loop : -1.75 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1077 TYR 0.009 0.001 TYR B 682 PHE 0.013 0.001 PHE D1048 TRP 0.007 0.001 TRP B 944 HIS 0.004 0.000 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00203 (38700) covalent geometry : angle 0.52142 (52912) hydrogen bonds : bond 0.03375 ( 1934) hydrogen bonds : angle 3.48270 ( 5655) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 177 time to evaluate : 1.642 Fit side-chains REVERT: A 887 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8171 (mm) REVERT: A 948 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7708 (t80) REVERT: B 887 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8176 (mm) REVERT: B 948 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7727 (t80) REVERT: C 887 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8173 (mm) REVERT: D 887 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8170 (mm) REVERT: D 948 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7671 (t80) outliers start: 63 outliers final: 38 residues processed: 231 average time/residue: 0.1860 time to fit residues: 79.1376 Evaluate side-chains 209 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 759 CYS Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 944 TRP Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 759 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 TRP Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 759 CYS Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 944 TRP Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1352 VAL Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 944 TRP Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 491 optimal weight: 2.9990 chunk 464 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 chunk 417 optimal weight: 2.9990 chunk 218 optimal weight: 40.0000 chunk 400 optimal weight: 2.9990 chunk 352 optimal weight: 20.0000 chunk 465 optimal weight: 5.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.080639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054534 restraints weight = 138613.122| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.49 r_work: 0.2805 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 38700 Z= 0.096 Angle : 0.530 13.672 52912 Z= 0.255 Chirality : 0.038 0.187 6208 Planarity : 0.004 0.046 6784 Dihedral : 4.029 41.979 5512 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 1.49 % Allowed : 17.02 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.12), residues: 5168 helix: 1.90 (0.10), residues: 2676 sheet: -1.71 (0.21), residues: 444 loop : -1.70 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1077 TYR 0.009 0.001 TYR D 682 PHE 0.027 0.001 PHE B 937 TRP 0.008 0.001 TRP A 743 HIS 0.004 0.000 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00215 (38700) covalent geometry : angle 0.53008 (52912) hydrogen bonds : bond 0.03407 ( 1934) hydrogen bonds : angle 3.49678 ( 5655) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 1.522 Fit side-chains REVERT: A 182 MET cc_start: 0.8480 (ptp) cc_final: 0.8201 (ptm) REVERT: A 887 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8131 (mm) REVERT: B 887 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8135 (mm) REVERT: B 948 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7679 (t80) REVERT: C 182 MET cc_start: 0.8475 (ptp) cc_final: 0.8192 (ptm) REVERT: C 887 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8137 (mm) REVERT: D 887 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8120 (mm) outliers start: 51 outliers final: 42 residues processed: 223 average time/residue: 0.1919 time to fit residues: 78.6522 Evaluate side-chains 218 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 944 TRP Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 TRP Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 944 TRP Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1352 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 944 TRP Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 280 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 501 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 373 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.078627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051943 restraints weight = 138182.158| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.37 r_work: 0.2752 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 38700 Z= 0.191 Angle : 0.580 13.626 52912 Z= 0.286 Chirality : 0.041 0.273 6208 Planarity : 0.004 0.047 6784 Dihedral : 4.215 42.180 5512 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.71 % Favored : 93.21 % Rotamer: Outliers : 1.64 % Allowed : 16.70 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 5168 helix: 1.84 (0.10), residues: 2696 sheet: -1.70 (0.23), residues: 396 loop : -1.73 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1077 TYR 0.015 0.001 TYR D 682 PHE 0.030 0.001 PHE D 937 TRP 0.012 0.001 TRP A 743 HIS 0.005 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00450 (38700) covalent geometry : angle 0.57967 (52912) hydrogen bonds : bond 0.04621 ( 1934) hydrogen bonds : angle 3.71133 ( 5655) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10336 Ramachandran restraints generated. 5168 Oldfield, 0 Emsley, 5168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 1.533 Fit side-chains REVERT: A 887 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8135 (mm) REVERT: A 948 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7737 (t80) REVERT: B 887 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 948 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 887 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8143 (mm) REVERT: D 887 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8132 (mm) REVERT: D 948 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7719 (t80) outliers start: 56 outliers final: 46 residues processed: 226 average time/residue: 0.1836 time to fit residues: 76.1126 Evaluate side-chains 224 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 944 TRP Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 944 TRP Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1377 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 944 TRP Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1262 VAL Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1352 VAL Chi-restraints excluded: chain C residue 1377 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 940 LEU Chi-restraints excluded: chain D residue 944 TRP Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1262 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 515 optimal weight: 30.0000 chunk 115 optimal weight: 8.9990 chunk 375 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 451 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** 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 = 0.3584 r_free = 0.3584 target = 0.077416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050592 restraints weight = 140183.108| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.38 r_work: 0.2713 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 38700 Z= 0.256 Angle : 0.639 13.224 52912 Z= 0.320 Chirality : 0.043 0.253 6208 Planarity : 0.004 0.047 6784 Dihedral : 4.566 41.634 5512 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.61 % Rotamer: Outliers : 1.81 % Allowed : 16.64 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 5168 helix: 1.80 (0.10), residues: 2648 sheet: -2.05 (0.22), residues: 404 loop : -1.81 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1077 TYR 0.019 0.001 TYR B 682 PHE 0.031 0.001 PHE C 937 TRP 0.013 0.001 TRP A 754 HIS 0.006 0.001 HIS D1068 Details of bonding type rmsd covalent geometry : bond 0.00604 (38700) covalent geometry : angle 0.63911 (52912) hydrogen bonds : bond 0.05496 ( 1934) hydrogen bonds : angle 3.98055 ( 5655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9555.27 seconds wall clock time: 164 minutes 25.07 seconds (9865.07 seconds total)