Starting phenix.real_space_refine on Sun Dec 29 20:18:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oh5_16878/12_2024/8oh5_16878_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oh5_16878/12_2024/8oh5_16878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oh5_16878/12_2024/8oh5_16878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oh5_16878/12_2024/8oh5_16878.map" model { file = "/net/cci-nas-00/data/ceres_data/8oh5_16878/12_2024/8oh5_16878_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oh5_16878/12_2024/8oh5_16878_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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: 7 Type Number sf(0) Gaussians Fe 168 7.16 5 Zn 4 6.06 5 P 32 5.49 5 S 616 5.16 5 C 36584 2.51 5 N 9956 2.21 5 O 11264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 58624 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1118 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "B" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4431 Classifications: {'peptide': 584} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 557} Chain: "C" Number of atoms: 8846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 8846 Classifications: {'peptide': 1172} Link IDs: {'PTRANS': 45, 'TRANS': 1126} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 153 Unusual residues: {'FAD': 1, 'FES': 1, 'NDP': 1, 'SF4': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 597 SG CYS A 93 112.975 46.921 31.349 1.00 39.21 S ATOM 628 SG CYS A 98 116.496 46.312 30.951 1.00 41.52 S ATOM 878 SG CYS A 134 111.818 46.355 35.099 1.00 43.97 S ATOM 902 SG CYS A 138 114.558 43.822 35.695 1.00 49.73 S ATOM 4324 SG CYS B 425 129.027 58.984 37.596 1.00 29.89 S ATOM 5065 SG CYS B 518 132.252 59.148 35.692 1.00 48.32 S ATOM 5098 SG CYS B 523 129.209 61.416 34.520 1.00 45.50 S ATOM 1188 SG CYS B 10 113.394 34.912 31.946 1.00 51.88 S ATOM 1443 SG CYS B 45 113.499 35.148 35.804 1.00 56.34 S ATOM 1417 SG CYS B 41 112.581 31.765 36.740 1.00 49.38 S ATOM 1443 SG CYS B 45 113.499 35.148 35.804 1.00 56.34 S ATOM 5272 SG CYS B 546 135.622 58.223 16.210 1.00 60.92 S ATOM 5445 SG CYS B 569 131.913 57.050 19.864 1.00 58.45 S ATOM 5272 SG CYS B 546 135.622 58.223 16.210 1.00 60.92 S ATOM 5423 SG CYS B 566 136.387 61.012 19.428 1.00 55.38 S ATOM 5203 SG CYS B 536 147.334 50.900 18.882 1.00 66.49 S ATOM 5243 SG CYS B 542 141.329 51.748 18.372 1.00 54.81 S ATOM 4464 SG CYS B 442 100.378 63.751 43.714 1.00 0.81 S ATOM 4509 SG CYS B 448 107.050 64.244 44.907 1.00 7.74 S ATOM 4820 SG CYS B 488 102.969 60.224 47.885 1.00 23.54 S ATOM 4483 SG CYS B 445 103.673 67.142 48.022 1.00 0.00 S ATOM 10587 SG CYS C 666 93.918 82.684 42.149 1.00 0.00 S ATOM 10212 SG CYS C 613 97.559 77.844 39.310 1.00 3.97 S ATOM 10251 SG CYS C 619 91.549 76.940 40.162 1.00 0.62 S ATOM 10233 SG CYS C 616 94.935 77.743 45.382 1.00 0.00 S ATOM 9785 SG CYS C 562 99.463 102.842 32.545 1.00 0.00 S ATOM 6698 SG CYS C 155 105.648 104.556 30.498 1.00 1.61 S ATOM 9808 SG CYS C 565 103.697 98.611 31.981 1.00 0.00 S ATOM 6324 SG CYS C 104 104.689 103.234 36.407 1.00 0.00 S ATOM 9875 SG CYS C 573 99.768 87.593 45.476 1.00 0.00 S ATOM 6293 SG CYS C 100 104.864 91.103 43.324 1.00 0.00 S ATOM 9818 SG CYS C 567 99.429 90.656 39.939 1.00 0.00 S ATOM 6671 SG CYS C 151 108.068 109.321 36.497 1.00 0.00 S ATOM 6641 SG CYS C 147 110.853 114.173 39.592 1.00 8.11 S ATOM 6351 SG CYS C 108 108.906 108.581 42.495 1.00 0.00 S ATOM 10540 SG CYS C 659 80.653 80.744 39.257 1.00 0.00 S ATOM 10520 SG CYS C 656 82.601 80.221 33.417 1.00 9.48 S ATOM 10282 SG CYS C 623 83.681 75.365 37.934 1.00 0.00 S ATOM 10559 SG CYS C 662 86.644 81.128 38.398 1.00 0.00 S ATOM 10776 SG CYS C 692 72.292 90.688 43.140 1.00 0.00 S ATOM 11031 SG CYS C 725 73.846 85.406 39.927 1.00 3.86 S ATOM 10798 SG CYS C 695 68.407 86.006 41.235 1.00 13.95 S ATOM 10819 SG CYS C 699 72.962 85.841 46.536 1.00 0.00 S ATOM 5814 SG CYS C 36 96.270 73.957 51.017 1.00 7.15 S ATOM 5903 SG CYS C 47 99.312 75.785 51.943 1.00 0.00 S ATOM 5921 SG CYS C 50 98.109 73.977 57.047 1.00 0.00 S ATOM 6024 SG CYS C 64 95.002 72.438 55.914 1.00 0.00 S Restraints were copied for chains: D, G, J, E, H, K, F, I, L Time building chain proxies: 26.56, per 1000 atoms: 0.45 Number of scatterers: 58624 At special positions: 0 Unit cell: (162.35, 262.65, 141.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Fe 168 26.01 S 616 16.00 P 32 15.00 O 11264 8.00 N 9956 7.00 C 36584 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.98 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 98 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 134 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 138 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 93 " pdb=" FES B 602 " pdb="FE2 FES B 602 " - pdb=" SG CYS B 41 " pdb="FE1 FES B 602 " - pdb=" SG CYS B 10 " pdb="FE2 FES B 602 " - pdb=" SG CYS B 45 " pdb=" FES C1209 " pdb="FE2 FES C1209 " - pdb=" SG CYS C 50 " pdb="FE1 FES C1209 " - pdb=" SG CYS C 47 " pdb="FE2 FES C1209 " - pdb=" SG CYS C 64 " pdb="FE1 FES C1209 " - pdb=" SG CYS C 36 " pdb=" FES D 201 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 98 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 134 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 93 " pdb=" FES E 602 " pdb="FE2 FES E 602 " - pdb=" SG CYS E 41 " pdb="FE1 FES E 602 " - pdb=" SG CYS E 10 " pdb="FE2 FES E 602 " - pdb=" SG CYS E 45 " pdb=" FES F1209 " pdb="FE2 FES F1209 " - pdb=" SG CYS F 50 " pdb="FE1 FES F1209 " - pdb=" SG CYS F 47 " pdb="FE2 FES F1209 " - pdb=" SG CYS F 64 " pdb="FE1 FES F1209 " - pdb=" SG CYS F 36 " pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 98 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 138 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 134 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 93 " pdb=" FES H 602 " pdb="FE2 FES H 602 " - pdb=" SG CYS H 41 " pdb="FE1 FES H 602 " - pdb=" SG CYS H 10 " pdb="FE2 FES H 602 " - pdb=" SG CYS H 45 " pdb=" FES I1209 " pdb="FE2 FES I1209 " - pdb=" SG CYS I 50 " pdb="FE1 FES I1209 " - pdb=" SG CYS I 47 " pdb="FE2 FES I1209 " - pdb=" SG CYS I 64 " pdb="FE1 FES I1209 " - pdb=" SG CYS I 36 " pdb=" FES J 201 " pdb="FE1 FES J 201 " - pdb=" SG CYS J 98 " pdb="FE2 FES J 201 " - pdb=" SG CYS J 134 " pdb="FE2 FES J 201 " - pdb=" SG CYS J 138 " pdb="FE1 FES J 201 " - pdb=" SG CYS J 93 " pdb=" FES K 602 " pdb="FE2 FES K 602 " - pdb=" SG CYS K 41 " pdb="FE1 FES K 602 " - pdb=" SG CYS K 10 " pdb="FE2 FES K 602 " - pdb=" SG CYS K 45 " pdb=" FES L1209 " pdb="FE2 FES L1209 " - pdb=" SG CYS L 50 " pdb="FE1 FES L1209 " - pdb=" SG CYS L 47 " pdb="FE2 FES L1209 " - pdb=" SG CYS L 64 " pdb="FE1 FES L1209 " - pdb=" SG CYS L 36 " pdb=" SF4 B 604 " pdb="FE3 SF4 B 604 " - pdb=" SG CYS B 569 " pdb="FE4 SF4 B 604 " - pdb=" SG CYS B 566 " pdb="FE4 SF4 B 604 " - pdb=" SG CYS B 546 " pdb=" SF4 B 605 " pdb="FE4 SF4 B 605 " - pdb=" ND1 HIS B 559 " pdb="FE1 SF4 B 605 " - pdb=" SG CYS B 536 " pdb="FE3 SF4 B 605 " - pdb=" SG CYS B 542 " pdb=" SF4 B 607 " pdb="FE4 SF4 B 607 " - pdb=" SG CYS B 445 " pdb="FE1 SF4 B 607 " - pdb=" SG CYS B 442 " pdb="FE2 SF4 B 607 " - pdb=" SG CYS B 448 " pdb="FE3 SF4 B 607 " - pdb=" SG CYS B 488 " pdb=" SF4 C1202 " pdb="FE2 SF4 C1202 " - pdb=" SG CYS C 613 " pdb="FE1 SF4 C1202 " - pdb=" SG CYS C 666 " pdb="FE4 SF4 C1202 " - pdb=" SG CYS C 616 " pdb="FE3 SF4 C1202 " - pdb=" SG CYS C 619 " pdb=" SF4 C1204 " pdb="FE1 SF4 C1204 " - pdb=" SG CYS C 562 " pdb="FE2 SF4 C1204 " - pdb=" SG CYS C 155 " pdb="FE3 SF4 C1204 " - pdb=" SG CYS C 565 " pdb="FE4 SF4 C1204 " - pdb=" SG CYS C 104 " pdb=" SF4 C1205 " pdb="FE4 SF4 C1205 " - pdb=" NE2 HIS C 96 " pdb="FE2 SF4 C1205 " - pdb=" SG CYS C 100 " pdb="FE1 SF4 C1205 " - pdb=" SG CYS C 573 " pdb="FE3 SF4 C1205 " - pdb=" SG CYS C 567 " pdb=" SF4 C1206 " pdb="FE2 SF4 C1206 " - pdb=" SG CYS C 147 " pdb="FE1 SF4 C1206 " - pdb=" SG CYS C 151 " pdb="FE3 SF4 C1206 " - pdb=" SG CYS C 108 " pdb=" SF4 C1207 " pdb="FE1 SF4 C1207 " - pdb=" SG CYS C 659 " pdb="FE2 SF4 C1207 " - pdb=" SG CYS C 656 " pdb="FE3 SF4 C1207 " - pdb=" SG CYS C 623 " pdb="FE4 SF4 C1207 " - pdb=" SG CYS C 662 " pdb=" SF4 C1208 " pdb="FE1 SF4 C1208 " - pdb=" SG CYS C 692 " pdb="FE2 SF4 C1208 " - pdb=" SG CYS C 725 " pdb="FE4 SF4 C1208 " - pdb=" SG CYS C 699 " pdb="FE3 SF4 C1208 " - pdb=" SG CYS C 695 " pdb=" SF4 E 604 " pdb="FE3 SF4 E 604 " - pdb=" SG CYS E 569 " pdb="FE4 SF4 E 604 " - pdb=" SG CYS E 566 " pdb="FE4 SF4 E 604 " - pdb=" SG CYS E 546 " pdb=" SF4 E 605 " pdb="FE4 SF4 E 605 " - pdb=" ND1 HIS E 559 " pdb="FE1 SF4 E 605 " - pdb=" SG CYS E 536 " pdb="FE3 SF4 E 605 " - pdb=" SG CYS E 542 " pdb=" SF4 E 607 " pdb="FE4 SF4 E 607 " - pdb=" SG CYS E 445 " pdb="FE1 SF4 E 607 " - pdb=" SG CYS E 442 " pdb="FE2 SF4 E 607 " - pdb=" SG CYS E 448 " pdb="FE3 SF4 E 607 " - pdb=" SG CYS E 488 " pdb=" SF4 F1202 " pdb="FE2 SF4 F1202 " - pdb=" SG CYS F 613 " pdb="FE1 SF4 F1202 " - pdb=" SG CYS F 666 " pdb="FE4 SF4 F1202 " - pdb=" SG CYS F 616 " pdb="FE3 SF4 F1202 " - pdb=" SG CYS F 619 " pdb=" SF4 F1204 " pdb="FE1 SF4 F1204 " - pdb=" SG CYS F 562 " pdb="FE2 SF4 F1204 " - pdb=" SG CYS F 155 " pdb="FE3 SF4 F1204 " - pdb=" SG CYS F 565 " pdb="FE4 SF4 F1204 " - pdb=" SG CYS F 104 " pdb=" SF4 F1205 " pdb="FE4 SF4 F1205 " - pdb=" NE2 HIS F 96 " pdb="FE2 SF4 F1205 " - pdb=" SG CYS F 100 " pdb="FE1 SF4 F1205 " - pdb=" SG CYS F 573 " pdb="FE3 SF4 F1205 " - pdb=" SG CYS F 567 " pdb=" SF4 F1206 " pdb="FE2 SF4 F1206 " - pdb=" SG CYS F 147 " pdb="FE1 SF4 F1206 " - pdb=" SG CYS F 151 " pdb="FE3 SF4 F1206 " - pdb=" SG CYS F 108 " pdb=" SF4 F1207 " pdb="FE1 SF4 F1207 " - pdb=" SG CYS F 659 " pdb="FE2 SF4 F1207 " - pdb=" SG CYS F 656 " pdb="FE3 SF4 F1207 " - pdb=" SG CYS F 623 " pdb="FE4 SF4 F1207 " - pdb=" SG CYS F 662 " pdb=" SF4 F1208 " pdb="FE1 SF4 F1208 " - pdb=" SG CYS F 692 " pdb="FE2 SF4 F1208 " - pdb=" SG CYS F 725 " pdb="FE4 SF4 F1208 " - pdb=" SG CYS F 699 " pdb="FE3 SF4 F1208 " - pdb=" SG CYS F 695 " pdb=" SF4 H 604 " pdb="FE3 SF4 H 604 " - pdb=" SG CYS H 569 " pdb="FE4 SF4 H 604 " - pdb=" SG CYS H 566 " pdb="FE4 SF4 H 604 " - pdb=" SG CYS H 546 " pdb=" SF4 H 605 " pdb="FE4 SF4 H 605 " - pdb=" ND1 HIS H 559 " pdb="FE1 SF4 H 605 " - pdb=" SG CYS H 536 " pdb="FE3 SF4 H 605 " - pdb=" SG CYS H 542 " pdb=" SF4 H 607 " pdb="FE4 SF4 H 607 " - pdb=" SG CYS H 445 " pdb="FE1 SF4 H 607 " - pdb=" SG CYS H 442 " pdb="FE2 SF4 H 607 " - pdb=" SG CYS H 448 " pdb="FE3 SF4 H 607 " - pdb=" SG CYS H 488 " pdb=" SF4 I1202 " pdb="FE1 SF4 I1202 " - pdb=" SG CYS I 666 " pdb="FE2 SF4 I1202 " - pdb=" SG CYS I 613 " pdb="FE4 SF4 I1202 " - pdb=" SG CYS I 616 " pdb="FE3 SF4 I1202 " - pdb=" SG CYS I 619 " pdb=" SF4 I1204 " pdb="FE1 SF4 I1204 " - pdb=" SG CYS I 562 " pdb="FE2 SF4 I1204 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I1204 " - pdb=" SG CYS I 565 " pdb="FE4 SF4 I1204 " - pdb=" SG CYS I 104 " pdb=" SF4 I1205 " pdb="FE4 SF4 I1205 " - pdb=" NE2 HIS I 96 " pdb="FE2 SF4 I1205 " - pdb=" SG CYS I 100 " pdb="FE1 SF4 I1205 " - pdb=" SG CYS I 573 " pdb="FE3 SF4 I1205 " - pdb=" SG CYS I 567 " pdb=" SF4 I1206 " pdb="FE2 SF4 I1206 " - pdb=" SG CYS I 147 " pdb="FE1 SF4 I1206 " - pdb=" SG CYS I 151 " pdb="FE3 SF4 I1206 " - pdb=" SG CYS I 108 " pdb=" SF4 I1207 " pdb="FE1 SF4 I1207 " - pdb=" SG CYS I 659 " pdb="FE2 SF4 I1207 " - pdb=" SG CYS I 656 " pdb="FE3 SF4 I1207 " - pdb=" SG CYS I 623 " pdb="FE4 SF4 I1207 " - pdb=" SG CYS I 662 " pdb=" SF4 I1208 " pdb="FE1 SF4 I1208 " - pdb=" SG CYS I 692 " pdb="FE2 SF4 I1208 " - pdb=" SG CYS I 725 " pdb="FE4 SF4 I1208 " - pdb=" SG CYS I 699 " pdb="FE3 SF4 I1208 " - pdb=" SG CYS I 695 " pdb=" SF4 K 604 " pdb="FE3 SF4 K 604 " - pdb=" SG CYS K 569 " pdb="FE4 SF4 K 604 " - pdb=" SG CYS K 566 " pdb="FE4 SF4 K 604 " - pdb=" SG CYS K 546 " pdb=" SF4 K 605 " pdb="FE4 SF4 K 605 " - pdb=" ND1 HIS K 559 " pdb="FE1 SF4 K 605 " - pdb=" SG CYS K 536 " pdb="FE3 SF4 K 605 " - pdb=" SG CYS K 542 " pdb=" SF4 K 607 " pdb="FE4 SF4 K 607 " - pdb=" SG CYS K 445 " pdb="FE1 SF4 K 607 " - pdb=" SG CYS K 442 " pdb="FE2 SF4 K 607 " - pdb=" SG CYS K 448 " pdb="FE3 SF4 K 607 " - pdb=" SG CYS K 488 " pdb=" SF4 L1202 " pdb="FE2 SF4 L1202 " - pdb=" SG CYS L 613 " pdb="FE1 SF4 L1202 " - pdb=" SG CYS L 666 " pdb="FE4 SF4 L1202 " - pdb=" SG CYS L 616 " pdb="FE3 SF4 L1202 " - pdb=" SG CYS L 619 " pdb=" SF4 L1204 " pdb="FE1 SF4 L1204 " - pdb=" SG CYS L 562 " pdb="FE2 SF4 L1204 " - pdb=" SG CYS L 155 " pdb="FE3 SF4 L1204 " - pdb=" SG CYS L 565 " pdb="FE4 SF4 L1204 " - pdb=" SG CYS L 104 " pdb=" SF4 L1205 " pdb="FE4 SF4 L1205 " - pdb=" NE2 HIS L 96 " pdb="FE2 SF4 L1205 " - pdb=" SG CYS L 100 " pdb="FE1 SF4 L1205 " - pdb=" SG CYS L 573 " pdb="FE3 SF4 L1205 " - pdb=" SG CYS L 567 " pdb=" SF4 L1206 " pdb="FE2 SF4 L1206 " - pdb=" SG CYS L 147 " pdb="FE1 SF4 L1206 " - pdb=" SG CYS L 151 " pdb="FE3 SF4 L1206 " - pdb=" SG CYS L 108 " pdb=" SF4 L1207 " pdb="FE1 SF4 L1207 " - pdb=" SG CYS L 659 " pdb="FE2 SF4 L1207 " - pdb=" SG CYS L 656 " pdb="FE3 SF4 L1207 " - pdb=" SG CYS L 623 " pdb="FE4 SF4 L1207 " - pdb=" SG CYS L 662 " pdb=" SF4 L1208 " pdb="FE1 SF4 L1208 " - pdb=" SG CYS L 692 " pdb="FE2 SF4 L1208 " - pdb=" SG CYS L 725 " pdb="FE4 SF4 L1208 " - pdb=" SG CYS L 699 " pdb="FE3 SF4 L1208 " - pdb=" SG CYS L 695 " Number of angles added : 440 Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 512 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 425 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 518 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 523 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 512 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 425 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 518 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 523 " pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" NE2 HIS H 512 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 425 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 518 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 523 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 512 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 425 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 518 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 523 " Number of angles added : 12 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13824 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 72 sheets defined 43.4% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.846A pdb=" N ILE A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.506A pdb=" N ALA B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.546A pdb=" N MET B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.843A pdb=" N LYS B 101 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.860A pdb=" N TYR B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.754A pdb=" N MET B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 199 through 215 removed outlier: 4.005A pdb=" N LEU B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 244 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.628A pdb=" N GLY B 253 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 309 through 323 removed outlier: 3.546A pdb=" N PHE B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Proline residue: B 317 - end of helix removed outlier: 3.799A pdb=" N ASN B 322 " --> pdb=" O TRP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 385 through 388 Processing helix chain 'B' and resid 401 through 408 Processing helix chain 'B' and resid 425 through 440 Processing helix chain 'B' and resid 445 through 463 removed outlier: 4.534A pdb=" N THR B 452 " --> pdb=" O CYS B 448 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 486 removed outlier: 3.556A pdb=" N SER B 481 " --> pdb=" O GLU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.501A pdb=" N GLN B 492 " --> pdb=" O CYS B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 505 through 514 removed outlier: 3.818A pdb=" N TYR B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 510 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.624A pdb=" N HIS C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 94 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.624A pdb=" N ALA C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 201 through 213 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.706A pdb=" N LEU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.697A pdb=" N LEU C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 331 through 344 Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 470 through 475 Processing helix chain 'C' and resid 478 through 498 removed outlier: 3.601A pdb=" N ALA C 482 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'C' and resid 535 through 540 removed outlier: 3.821A pdb=" N ASN C 540 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 560 Processing helix chain 'C' and resid 574 through 582 Processing helix chain 'C' and resid 610 through 613 removed outlier: 3.528A pdb=" N CYS C 613 " --> pdb=" O PRO C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 617 through 626 Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 654 removed outlier: 3.795A pdb=" N THR C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 666 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 732 through 737 removed outlier: 3.547A pdb=" N ALA C 735 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 776 Processing helix chain 'C' and resid 789 through 803 Processing helix chain 'C' and resid 818 through 824 removed outlier: 4.078A pdb=" N VAL C 822 " --> pdb=" O GLY C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 835 Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 851 through 862 removed outlier: 3.606A pdb=" N ASP C 855 " --> pdb=" O HIS C 851 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 862 " --> pdb=" O ILE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 888 removed outlier: 3.679A pdb=" N MET C 878 " --> pdb=" O ASN C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 898 removed outlier: 3.685A pdb=" N VAL C 895 " --> pdb=" O ASP C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 915 through 928 removed outlier: 3.576A pdb=" N ALA C 928 " --> pdb=" O LYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 956 removed outlier: 3.506A pdb=" N VAL C 945 " --> pdb=" O SER C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 985 through 995 removed outlier: 3.852A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1010 removed outlier: 3.899A pdb=" N ALA C1010 " --> pdb=" O ASP C1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1007 through 1010' Processing helix chain 'C' and resid 1011 through 1019 Processing helix chain 'C' and resid 1032 through 1037 removed outlier: 3.641A pdb=" N ALA C1037 " --> pdb=" O LYS C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1050 removed outlier: 3.866A pdb=" N VAL C1050 " --> pdb=" O SER C1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1088 Processing helix chain 'C' and resid 1093 through 1105 removed outlier: 3.627A pdb=" N VAL C1097 " --> pdb=" O THR C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1170 removed outlier: 3.742A pdb=" N GLN C1170 " --> pdb=" O VAL C1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 Proline residue: D 25 - end of helix Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 102 through 115 removed outlier: 3.845A pdb=" N ILE D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 155 through 167 Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.506A pdb=" N ALA E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.547A pdb=" N MET E 20 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 77 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.843A pdb=" N LYS E 101 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.859A pdb=" N TYR E 121 " --> pdb=" O ASN E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.754A pdb=" N MET E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 199 through 215 removed outlier: 4.006A pdb=" N LEU E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 244 Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.628A pdb=" N GLY E 253 " --> pdb=" O ASN E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 282 Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 309 through 323 removed outlier: 3.546A pdb=" N PHE E 313 " --> pdb=" O ASN E 309 " (cutoff:3.500A) Proline residue: E 317 - end of helix removed outlier: 3.799A pdb=" N ASN E 322 " --> pdb=" O TRP E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 366 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 385 through 388 Processing helix chain 'E' and resid 401 through 408 Processing helix chain 'E' and resid 425 through 440 Processing helix chain 'E' and resid 445 through 463 removed outlier: 4.534A pdb=" N THR E 452 " --> pdb=" O CYS E 448 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS E 453 " --> pdb=" O ARG E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 486 removed outlier: 3.556A pdb=" N SER E 481 " --> pdb=" O GLU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 493 removed outlier: 3.501A pdb=" N GLN E 492 " --> pdb=" O CYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 502 Processing helix chain 'E' and resid 505 through 514 removed outlier: 3.818A pdb=" N TYR E 509 " --> pdb=" O PHE E 505 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 510 " --> pdb=" O ARG E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 545 Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.624A pdb=" N HIS F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 94 Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.624A pdb=" N ALA F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 165 through 179 Processing helix chain 'F' and resid 201 through 213 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 241 through 255 removed outlier: 3.706A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET F 255 " --> pdb=" O LEU F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 278 removed outlier: 3.697A pdb=" N LEU F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 331 through 344 Processing helix chain 'F' and resid 363 through 374 Processing helix chain 'F' and resid 470 through 475 Processing helix chain 'F' and resid 478 through 498 removed outlier: 3.601A pdb=" N ALA F 482 " --> pdb=" O ILE F 478 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 521 Processing helix chain 'F' and resid 535 through 540 removed outlier: 3.820A pdb=" N ASN F 540 " --> pdb=" O ALA F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 560 Processing helix chain 'F' and resid 574 through 582 Processing helix chain 'F' and resid 610 through 613 removed outlier: 3.528A pdb=" N CYS F 613 " --> pdb=" O PRO F 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 610 through 613' Processing helix chain 'F' and resid 617 through 626 Processing helix chain 'F' and resid 637 through 641 Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 650 through 654 removed outlier: 3.795A pdb=" N THR F 654 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 666 Processing helix chain 'F' and resid 725 through 731 Processing helix chain 'F' and resid 732 through 737 removed outlier: 3.547A pdb=" N ALA F 735 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 756 through 776 Processing helix chain 'F' and resid 789 through 803 Processing helix chain 'F' and resid 818 through 824 removed outlier: 4.078A pdb=" N VAL F 822 " --> pdb=" O GLY F 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 835 Processing helix chain 'F' and resid 846 through 851 Processing helix chain 'F' and resid 851 through 862 removed outlier: 3.607A pdb=" N ASP F 855 " --> pdb=" O HIS F 851 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 862 " --> pdb=" O ILE F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 874 through 888 removed outlier: 3.678A pdb=" N MET F 878 " --> pdb=" O ASN F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 898 removed outlier: 3.685A pdb=" N VAL F 895 " --> pdb=" O ASP F 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 909 Processing helix chain 'F' and resid 915 through 928 removed outlier: 3.577A pdb=" N ALA F 928 " --> pdb=" O LYS F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 941 through 956 removed outlier: 3.506A pdb=" N VAL F 945 " --> pdb=" O SER F 941 " (cutoff:3.500A) Processing helix chain 'F' and resid 973 through 980 Processing helix chain 'F' and resid 985 through 995 removed outlier: 3.852A pdb=" N VAL F 989 " --> pdb=" O PRO F 985 " (cutoff:3.500A) Processing helix chain 'F' and resid 1007 through 1010 removed outlier: 3.900A pdb=" N ALA F1010 " --> pdb=" O ASP F1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1007 through 1010' Processing helix chain 'F' and resid 1011 through 1019 Processing helix chain 'F' and resid 1032 through 1037 removed outlier: 3.641A pdb=" N ALA F1037 " --> pdb=" O LYS F1033 " (cutoff:3.500A) Processing helix chain 'F' and resid 1046 through 1050 removed outlier: 3.866A pdb=" N VAL F1050 " --> pdb=" O SER F1047 " (cutoff:3.500A) Processing helix chain 'F' and resid 1075 through 1088 Processing helix chain 'F' and resid 1093 through 1105 removed outlier: 3.627A pdb=" N VAL F1097 " --> pdb=" O THR F1093 " (cutoff:3.500A) Processing helix chain 'F' and resid 1159 through 1170 removed outlier: 3.743A pdb=" N GLN F1170 " --> pdb=" O VAL F1166 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 Proline residue: G 25 - end of helix Processing helix chain 'G' and resid 36 through 49 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 66 through 76 Processing helix chain 'G' and resid 95 through 101 Processing helix chain 'G' and resid 102 through 115 removed outlier: 3.846A pdb=" N ILE G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 141 Processing helix chain 'G' and resid 155 through 167 Processing helix chain 'H' and resid 8 through 13 removed outlier: 3.506A pdb=" N ALA H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.546A pdb=" N MET H 20 " --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 77 Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.843A pdb=" N LYS H 101 " --> pdb=" O ILE H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 124 removed outlier: 3.860A pdb=" N TYR H 121 " --> pdb=" O ASN H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.755A pdb=" N MET H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 164 through 171 Processing helix chain 'H' and resid 190 through 199 Processing helix chain 'H' and resid 199 through 215 removed outlier: 4.005A pdb=" N LEU H 203 " --> pdb=" O ASP H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 244 Processing helix chain 'H' and resid 250 through 254 removed outlier: 3.628A pdb=" N GLY H 253 " --> pdb=" O ASN H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 282 Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 309 through 323 removed outlier: 3.546A pdb=" N PHE H 313 " --> pdb=" O ASN H 309 " (cutoff:3.500A) Proline residue: H 317 - end of helix removed outlier: 3.799A pdb=" N ASN H 322 " --> pdb=" O TRP H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 366 Processing helix chain 'H' and resid 372 through 376 Processing helix chain 'H' and resid 385 through 388 Processing helix chain 'H' and resid 401 through 408 Processing helix chain 'H' and resid 425 through 440 Processing helix chain 'H' and resid 445 through 463 removed outlier: 4.534A pdb=" N THR H 452 " --> pdb=" O CYS H 448 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS H 453 " --> pdb=" O ARG H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 486 removed outlier: 3.556A pdb=" N SER H 481 " --> pdb=" O GLU H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 493 removed outlier: 3.501A pdb=" N GLN H 492 " --> pdb=" O CYS H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 502 Processing helix chain 'H' and resid 505 through 514 removed outlier: 3.818A pdb=" N TYR H 509 " --> pdb=" O PHE H 505 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 510 " --> pdb=" O ARG H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 545 Processing helix chain 'I' and resid 20 through 28 removed outlier: 3.624A pdb=" N HIS I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 94 Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 113 through 122 Processing helix chain 'I' and resid 125 through 134 removed outlier: 3.624A pdb=" N ALA I 129 " --> pdb=" O GLN I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 147 Processing helix chain 'I' and resid 155 through 160 Processing helix chain 'I' and resid 165 through 179 Processing helix chain 'I' and resid 201 through 213 Processing helix chain 'I' and resid 229 through 234 Processing helix chain 'I' and resid 241 through 255 removed outlier: 3.706A pdb=" N LEU I 245 " --> pdb=" O ASP I 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET I 255 " --> pdb=" O LEU I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 278 removed outlier: 3.697A pdb=" N LEU I 274 " --> pdb=" O SER I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 315 Processing helix chain 'I' and resid 331 through 344 Processing helix chain 'I' and resid 363 through 374 Processing helix chain 'I' and resid 470 through 475 Processing helix chain 'I' and resid 478 through 498 removed outlier: 3.602A pdb=" N ALA I 482 " --> pdb=" O ILE I 478 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN I 498 " --> pdb=" O ASP I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 521 Processing helix chain 'I' and resid 535 through 540 removed outlier: 3.821A pdb=" N ASN I 540 " --> pdb=" O ALA I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 560 Processing helix chain 'I' and resid 574 through 582 Processing helix chain 'I' and resid 610 through 613 removed outlier: 3.528A pdb=" N CYS I 613 " --> pdb=" O PRO I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 617 through 626 Processing helix chain 'I' and resid 637 through 641 Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 650 through 654 removed outlier: 3.796A pdb=" N THR I 654 " --> pdb=" O LEU I 651 " (cutoff:3.500A) Processing helix chain 'I' and resid 660 through 666 Processing helix chain 'I' and resid 725 through 731 Processing helix chain 'I' and resid 732 through 737 removed outlier: 3.547A pdb=" N ALA I 735 " --> pdb=" O LEU I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 776 Processing helix chain 'I' and resid 789 through 803 Processing helix chain 'I' and resid 818 through 824 removed outlier: 4.078A pdb=" N VAL I 822 " --> pdb=" O GLY I 818 " (cutoff:3.500A) Processing helix chain 'I' and resid 831 through 835 Processing helix chain 'I' and resid 846 through 851 Processing helix chain 'I' and resid 851 through 862 removed outlier: 3.607A pdb=" N ASP I 855 " --> pdb=" O HIS I 851 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY I 862 " --> pdb=" O ILE I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 874 through 888 removed outlier: 3.678A pdb=" N MET I 878 " --> pdb=" O ASN I 874 " (cutoff:3.500A) Processing helix chain 'I' and resid 891 through 898 removed outlier: 3.685A pdb=" N VAL I 895 " --> pdb=" O ASP I 891 " (cutoff:3.500A) Processing helix chain 'I' and resid 901 through 909 Processing helix chain 'I' and resid 915 through 928 removed outlier: 3.577A pdb=" N ALA I 928 " --> pdb=" O LYS I 924 " (cutoff:3.500A) Processing helix chain 'I' and resid 941 through 956 removed outlier: 3.506A pdb=" N VAL I 945 " --> pdb=" O SER I 941 " (cutoff:3.500A) Processing helix chain 'I' and resid 973 through 980 Processing helix chain 'I' and resid 985 through 995 removed outlier: 3.852A pdb=" N VAL I 989 " --> pdb=" O PRO I 985 " (cutoff:3.500A) Processing helix chain 'I' and resid 1007 through 1010 removed outlier: 3.900A pdb=" N ALA I1010 " --> pdb=" O ASP I1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1007 through 1010' Processing helix chain 'I' and resid 1011 through 1019 Processing helix chain 'I' and resid 1032 through 1037 removed outlier: 3.641A pdb=" N ALA I1037 " --> pdb=" O LYS I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1046 through 1050 removed outlier: 3.866A pdb=" N VAL I1050 " --> pdb=" O SER I1047 " (cutoff:3.500A) Processing helix chain 'I' and resid 1075 through 1088 Processing helix chain 'I' and resid 1093 through 1105 removed outlier: 3.627A pdb=" N VAL I1097 " --> pdb=" O THR I1093 " (cutoff:3.500A) Processing helix chain 'I' and resid 1159 through 1170 removed outlier: 3.741A pdb=" N GLN I1170 " --> pdb=" O VAL I1166 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 30 Proline residue: J 25 - end of helix Processing helix chain 'J' and resid 36 through 49 Processing helix chain 'J' and resid 52 through 61 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 95 through 101 Processing helix chain 'J' and resid 102 through 115 removed outlier: 3.846A pdb=" N ILE J 106 " --> pdb=" O GLY J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 141 Processing helix chain 'J' and resid 155 through 167 Processing helix chain 'K' and resid 8 through 13 removed outlier: 3.505A pdb=" N ALA K 13 " --> pdb=" O SER K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 31 removed outlier: 3.547A pdb=" N MET K 20 " --> pdb=" O GLY K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 77 Processing helix chain 'K' and resid 97 through 101 removed outlier: 3.843A pdb=" N LYS K 101 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.860A pdb=" N TYR K 121 " --> pdb=" O ASN K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 137 removed outlier: 3.754A pdb=" N MET K 137 " --> pdb=" O ALA K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 149 Processing helix chain 'K' and resid 160 through 163 Processing helix chain 'K' and resid 164 through 171 Processing helix chain 'K' and resid 190 through 199 Processing helix chain 'K' and resid 199 through 215 removed outlier: 4.006A pdb=" N LEU K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 244 Processing helix chain 'K' and resid 250 through 254 removed outlier: 3.629A pdb=" N GLY K 253 " --> pdb=" O ASN K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 282 Processing helix chain 'K' and resid 299 through 303 Processing helix chain 'K' and resid 309 through 323 removed outlier: 3.546A pdb=" N PHE K 313 " --> pdb=" O ASN K 309 " (cutoff:3.500A) Proline residue: K 317 - end of helix removed outlier: 3.799A pdb=" N ASN K 322 " --> pdb=" O TRP K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 366 Processing helix chain 'K' and resid 372 through 376 Processing helix chain 'K' and resid 385 through 388 Processing helix chain 'K' and resid 401 through 408 Processing helix chain 'K' and resid 425 through 440 Processing helix chain 'K' and resid 445 through 463 removed outlier: 4.534A pdb=" N THR K 452 " --> pdb=" O CYS K 448 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS K 453 " --> pdb=" O ARG K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 486 removed outlier: 3.556A pdb=" N SER K 481 " --> pdb=" O GLU K 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 493 removed outlier: 3.501A pdb=" N GLN K 492 " --> pdb=" O CYS K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 502 Processing helix chain 'K' and resid 505 through 514 removed outlier: 3.817A pdb=" N TYR K 509 " --> pdb=" O PHE K 505 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU K 510 " --> pdb=" O ARG K 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 545 Processing helix chain 'L' and resid 20 through 28 removed outlier: 3.624A pdb=" N HIS L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 94 Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 113 through 122 Processing helix chain 'L' and resid 125 through 134 removed outlier: 3.624A pdb=" N ALA L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 147 Processing helix chain 'L' and resid 155 through 160 Processing helix chain 'L' and resid 165 through 179 Processing helix chain 'L' and resid 201 through 213 Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'L' and resid 241 through 255 removed outlier: 3.706A pdb=" N LEU L 245 " --> pdb=" O ASP L 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET L 255 " --> pdb=" O LEU L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 278 removed outlier: 3.697A pdb=" N LEU L 274 " --> pdb=" O SER L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 315 Processing helix chain 'L' and resid 331 through 344 Processing helix chain 'L' and resid 363 through 374 Processing helix chain 'L' and resid 470 through 475 Processing helix chain 'L' and resid 478 through 498 removed outlier: 3.601A pdb=" N ALA L 482 " --> pdb=" O ILE L 478 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN L 498 " --> pdb=" O ASP L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 521 Processing helix chain 'L' and resid 535 through 540 removed outlier: 3.821A pdb=" N ASN L 540 " --> pdb=" O ALA L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 560 Processing helix chain 'L' and resid 574 through 582 Processing helix chain 'L' and resid 610 through 613 removed outlier: 3.528A pdb=" N CYS L 613 " --> pdb=" O PRO L 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 610 through 613' Processing helix chain 'L' and resid 617 through 626 Processing helix chain 'L' and resid 637 through 641 Processing helix chain 'L' and resid 647 through 649 No H-bonds generated for 'chain 'L' and resid 647 through 649' Processing helix chain 'L' and resid 650 through 654 removed outlier: 3.795A pdb=" N THR L 654 " --> pdb=" O LEU L 651 " (cutoff:3.500A) Processing helix chain 'L' and resid 660 through 666 Processing helix chain 'L' and resid 725 through 731 Processing helix chain 'L' and resid 732 through 737 removed outlier: 3.547A pdb=" N ALA L 735 " --> pdb=" O LEU L 732 " (cutoff:3.500A) Processing helix chain 'L' and resid 756 through 776 Processing helix chain 'L' and resid 789 through 803 Processing helix chain 'L' and resid 818 through 824 removed outlier: 4.078A pdb=" N VAL L 822 " --> pdb=" O GLY L 818 " (cutoff:3.500A) Processing helix chain 'L' and resid 831 through 835 Processing helix chain 'L' and resid 846 through 851 Processing helix chain 'L' and resid 851 through 862 removed outlier: 3.606A pdb=" N ASP L 855 " --> pdb=" O HIS L 851 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY L 862 " --> pdb=" O ILE L 858 " (cutoff:3.500A) Processing helix chain 'L' and resid 874 through 888 removed outlier: 3.678A pdb=" N MET L 878 " --> pdb=" O ASN L 874 " (cutoff:3.500A) Processing helix chain 'L' and resid 891 through 898 removed outlier: 3.686A pdb=" N VAL L 895 " --> pdb=" O ASP L 891 " (cutoff:3.500A) Processing helix chain 'L' and resid 901 through 909 Processing helix chain 'L' and resid 915 through 928 removed outlier: 3.576A pdb=" N ALA L 928 " --> pdb=" O LYS L 924 " (cutoff:3.500A) Processing helix chain 'L' and resid 941 through 956 removed outlier: 3.506A pdb=" N VAL L 945 " --> pdb=" O SER L 941 " (cutoff:3.500A) Processing helix chain 'L' and resid 973 through 980 Processing helix chain 'L' and resid 985 through 995 removed outlier: 3.852A pdb=" N VAL L 989 " --> pdb=" O PRO L 985 " (cutoff:3.500A) Processing helix chain 'L' and resid 1007 through 1010 removed outlier: 3.899A pdb=" N ALA L1010 " --> pdb=" O ASP L1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1007 through 1010' Processing helix chain 'L' and resid 1011 through 1019 Processing helix chain 'L' and resid 1032 through 1037 removed outlier: 3.641A pdb=" N ALA L1037 " --> pdb=" O LYS L1033 " (cutoff:3.500A) Processing helix chain 'L' and resid 1046 through 1050 removed outlier: 3.865A pdb=" N VAL L1050 " --> pdb=" O SER L1047 " (cutoff:3.500A) Processing helix chain 'L' and resid 1075 through 1088 Processing helix chain 'L' and resid 1093 through 1105 removed outlier: 3.626A pdb=" N VAL L1097 " --> pdb=" O THR L1093 " (cutoff:3.500A) Processing helix chain 'L' and resid 1159 through 1170 removed outlier: 3.741A pdb=" N GLN L1170 " --> pdb=" O VAL L1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.954A pdb=" N LYS B 2 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.689A pdb=" N GLY B 219 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS B 263 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 221 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY B 265 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS B 223 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 178 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 222 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B 180 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ARG B 224 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ALA B 182 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 355 removed outlier: 7.217A pdb=" N MET B 417 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA B 342 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 419 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA B 344 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASP B 421 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 528 through 531 Processing sheet with id=AA6, first strand: chain 'B' and resid 551 through 552 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 14 removed outlier: 9.265A pdb=" N ILE C 74 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN C 7 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 258 through 260 removed outlier: 6.744A pdb=" N VAL C 218 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE C 260 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 220 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL C 281 " --> pdb=" O PHE C 467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AB1, first strand: chain 'C' and resid 303 through 305 removed outlier: 6.743A pdb=" N LEU C 304 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS C 324 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE C 429 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 326 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 325 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 352 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C 327 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 349 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN C 378 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE C 351 " --> pdb=" O GLN C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 381 through 389 removed outlier: 6.829A pdb=" N LYS C 397 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL C 386 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA C 395 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY C 388 " --> pdb=" O ALA C 393 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 393 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU C 419 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ARG C 402 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR C 417 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 606 through 608 Processing sheet with id=AB4, first strand: chain 'C' and resid 632 through 635 Processing sheet with id=AB5, first strand: chain 'C' and resid 686 through 691 Processing sheet with id=AB6, first strand: chain 'C' and resid 751 through 754 removed outlier: 6.723A pdb=" N LEU C1024 " --> pdb=" O MET C1040 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL C1042 " --> pdb=" O LEU C1024 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C1026 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY C 781 " --> pdb=" O VAL C1002 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE C1004 " --> pdb=" O GLY C 781 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 783 " --> pdb=" O ILE C1004 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 780 " --> pdb=" O ILE C 807 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR C 809 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 782 " --> pdb=" O THR C 809 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL C 841 " --> pdb=" O VAL C 866 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 966 " --> pdb=" O PRO C 931 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE C 933 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 968 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 935 " --> pdb=" O VAL C 968 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 899 through 900 Processing sheet with id=AB9, first strand: chain 'C' and resid 1052 through 1055 Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 132 Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.955A pdb=" N LYS E 2 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 265 removed outlier: 6.689A pdb=" N GLY E 219 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS E 263 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE E 221 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY E 265 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS E 223 " --> pdb=" O GLY E 265 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL E 178 " --> pdb=" O HIS E 220 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR E 222 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS E 180 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ARG E 224 " --> pdb=" O CYS E 180 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ALA E 182 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 351 through 355 removed outlier: 7.218A pdb=" N MET E 417 " --> pdb=" O VAL E 340 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA E 342 " --> pdb=" O MET E 417 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL E 419 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA E 344 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASP E 421 " --> pdb=" O ALA E 344 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 528 through 531 Processing sheet with id=AC6, first strand: chain 'E' and resid 551 through 552 Processing sheet with id=AC7, first strand: chain 'F' and resid 11 through 14 removed outlier: 9.265A pdb=" N ILE F 74 " --> pdb=" O SER F 5 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN F 7 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 258 through 260 removed outlier: 6.745A pdb=" N VAL F 218 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE F 260 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE F 220 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL F 281 " --> pdb=" O PHE F 467 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AD1, first strand: chain 'F' and resid 303 through 305 removed outlier: 6.743A pdb=" N LEU F 304 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS F 324 " --> pdb=" O ARG F 427 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE F 429 " --> pdb=" O LYS F 324 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 326 " --> pdb=" O ILE F 429 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL F 325 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE F 352 " --> pdb=" O VAL F 325 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 327 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL F 349 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN F 378 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE F 351 " --> pdb=" O GLN F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 381 through 389 removed outlier: 6.829A pdb=" N LYS F 397 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL F 386 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA F 395 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY F 388 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA F 393 " --> pdb=" O GLY F 388 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU F 419 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ARG F 402 " --> pdb=" O THR F 417 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR F 417 " --> pdb=" O ARG F 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 606 through 608 Processing sheet with id=AD4, first strand: chain 'F' and resid 632 through 635 Processing sheet with id=AD5, first strand: chain 'F' and resid 686 through 691 Processing sheet with id=AD6, first strand: chain 'F' and resid 751 through 754 removed outlier: 6.723A pdb=" N LEU F1024 " --> pdb=" O MET F1040 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL F1042 " --> pdb=" O LEU F1024 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL F1026 " --> pdb=" O VAL F1042 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY F 781 " --> pdb=" O VAL F1002 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE F1004 " --> pdb=" O GLY F 781 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL F 783 " --> pdb=" O ILE F1004 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE F 780 " --> pdb=" O ILE F 807 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR F 809 " --> pdb=" O ILE F 780 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL F 782 " --> pdb=" O THR F 809 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL F 841 " --> pdb=" O VAL F 866 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 966 " --> pdb=" O PRO F 931 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE F 933 " --> pdb=" O ILE F 966 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL F 968 " --> pdb=" O ILE F 933 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE F 935 " --> pdb=" O VAL F 968 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 899 through 900 Processing sheet with id=AD9, first strand: chain 'F' and resid 1052 through 1055 Processing sheet with id=AE1, first strand: chain 'G' and resid 127 through 132 Processing sheet with id=AE2, first strand: chain 'H' and resid 35 through 38 removed outlier: 3.954A pdb=" N LYS H 2 " --> pdb=" O PHE H 54 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 259 through 265 removed outlier: 6.690A pdb=" N GLY H 219 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS H 263 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE H 221 " --> pdb=" O LYS H 263 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY H 265 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS H 223 " --> pdb=" O GLY H 265 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL H 178 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR H 222 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS H 180 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ARG H 224 " --> pdb=" O CYS H 180 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ALA H 182 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 351 through 355 removed outlier: 7.218A pdb=" N MET H 417 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA H 342 " --> pdb=" O MET H 417 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL H 419 " --> pdb=" O ALA H 342 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA H 344 " --> pdb=" O VAL H 419 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASP H 421 " --> pdb=" O ALA H 344 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 528 through 531 Processing sheet with id=AE6, first strand: chain 'H' and resid 551 through 552 Processing sheet with id=AE7, first strand: chain 'I' and resid 11 through 14 removed outlier: 9.265A pdb=" N ILE I 74 " --> pdb=" O SER I 5 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN I 7 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 258 through 260 removed outlier: 6.745A pdb=" N VAL I 218 " --> pdb=" O GLU I 258 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE I 260 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE I 220 " --> pdb=" O ILE I 260 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL I 281 " --> pdb=" O PHE I 467 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AF1, first strand: chain 'I' and resid 303 through 305 removed outlier: 6.743A pdb=" N LEU I 304 " --> pdb=" O ALA I 430 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS I 324 " --> pdb=" O ARG I 427 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE I 429 " --> pdb=" O LYS I 324 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU I 326 " --> pdb=" O ILE I 429 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL I 325 " --> pdb=" O THR I 350 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE I 352 " --> pdb=" O VAL I 325 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL I 327 " --> pdb=" O ILE I 352 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL I 349 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN I 378 " --> pdb=" O VAL I 349 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE I 351 " --> pdb=" O GLN I 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'I' and resid 381 through 389 removed outlier: 6.830A pdb=" N LYS I 397 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL I 386 " --> pdb=" O ALA I 395 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA I 395 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY I 388 " --> pdb=" O ALA I 393 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA I 393 " --> pdb=" O GLY I 388 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU I 419 " --> pdb=" O ILE I 400 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ARG I 402 " --> pdb=" O THR I 417 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR I 417 " --> pdb=" O ARG I 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 606 through 608 Processing sheet with id=AF4, first strand: chain 'I' and resid 632 through 635 Processing sheet with id=AF5, first strand: chain 'I' and resid 686 through 691 Processing sheet with id=AF6, first strand: chain 'I' and resid 751 through 754 removed outlier: 6.723A pdb=" N LEU I1024 " --> pdb=" O MET I1040 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL I1042 " --> pdb=" O LEU I1024 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL I1026 " --> pdb=" O VAL I1042 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY I 781 " --> pdb=" O VAL I1002 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE I1004 " --> pdb=" O GLY I 781 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL I 783 " --> pdb=" O ILE I1004 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE I 780 " --> pdb=" O ILE I 807 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR I 809 " --> pdb=" O ILE I 780 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL I 782 " --> pdb=" O THR I 809 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL I 841 " --> pdb=" O VAL I 866 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE I 966 " --> pdb=" O PRO I 931 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE I 933 " --> pdb=" O ILE I 966 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL I 968 " --> pdb=" O ILE I 933 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE I 935 " --> pdb=" O VAL I 968 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 899 through 900 Processing sheet with id=AF9, first strand: chain 'I' and resid 1052 through 1055 Processing sheet with id=AG1, first strand: chain 'J' and resid 127 through 132 Processing sheet with id=AG2, first strand: chain 'K' and resid 35 through 38 removed outlier: 3.955A pdb=" N LYS K 2 " --> pdb=" O PHE K 54 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 259 through 265 removed outlier: 6.690A pdb=" N GLY K 219 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS K 263 " --> pdb=" O GLY K 219 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE K 221 " --> pdb=" O LYS K 263 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY K 265 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS K 223 " --> pdb=" O GLY K 265 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL K 178 " --> pdb=" O HIS K 220 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR K 222 " --> pdb=" O VAL K 178 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS K 180 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ARG K 224 " --> pdb=" O CYS K 180 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ALA K 182 " --> pdb=" O ARG K 224 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 351 through 355 removed outlier: 7.217A pdb=" N MET K 417 " --> pdb=" O VAL K 340 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA K 342 " --> pdb=" O MET K 417 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL K 419 " --> pdb=" O ALA K 342 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA K 344 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASP K 421 " --> pdb=" O ALA K 344 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 528 through 531 Processing sheet with id=AG6, first strand: chain 'K' and resid 551 through 552 Processing sheet with id=AG7, first strand: chain 'L' and resid 11 through 14 removed outlier: 9.266A pdb=" N ILE L 74 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN L 7 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 258 through 260 removed outlier: 6.745A pdb=" N VAL L 218 " --> pdb=" O GLU L 258 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE L 260 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE L 220 " --> pdb=" O ILE L 260 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL L 281 " --> pdb=" O PHE L 467 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 289 through 290 Processing sheet with id=AH1, first strand: chain 'L' and resid 303 through 305 removed outlier: 6.743A pdb=" N LEU L 304 " --> pdb=" O ALA L 430 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS L 324 " --> pdb=" O ARG L 427 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE L 429 " --> pdb=" O LYS L 324 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU L 326 " --> pdb=" O ILE L 429 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL L 325 " --> pdb=" O THR L 350 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE L 352 " --> pdb=" O VAL L 325 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL L 327 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL L 349 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN L 378 " --> pdb=" O VAL L 349 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE L 351 " --> pdb=" O GLN L 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'L' and resid 381 through 389 removed outlier: 6.829A pdb=" N LYS L 397 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL L 386 " --> pdb=" O ALA L 395 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA L 395 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY L 388 " --> pdb=" O ALA L 393 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA L 393 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU L 419 " --> pdb=" O ILE L 400 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ARG L 402 " --> pdb=" O THR L 417 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR L 417 " --> pdb=" O ARG L 402 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 606 through 608 Processing sheet with id=AH4, first strand: chain 'L' and resid 632 through 635 Processing sheet with id=AH5, first strand: chain 'L' and resid 686 through 691 Processing sheet with id=AH6, first strand: chain 'L' and resid 751 through 754 removed outlier: 6.723A pdb=" N LEU L1024 " --> pdb=" O MET L1040 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL L1042 " --> pdb=" O LEU L1024 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL L1026 " --> pdb=" O VAL L1042 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY L 781 " --> pdb=" O VAL L1002 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE L1004 " --> pdb=" O GLY L 781 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL L 783 " --> pdb=" O ILE L1004 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE L 780 " --> pdb=" O ILE L 807 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR L 809 " --> pdb=" O ILE L 780 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL L 782 " --> pdb=" O THR L 809 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 865 through 867 removed outlier: 6.222A pdb=" N VAL L 841 " --> pdb=" O VAL L 866 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE L 966 " --> pdb=" O PRO L 931 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE L 933 " --> pdb=" O ILE L 966 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL L 968 " --> pdb=" O ILE L 933 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE L 935 " --> pdb=" O VAL L 968 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 899 through 900 Processing sheet with id=AH9, first strand: chain 'L' and resid 1052 through 1055 2280 hydrogen bonds defined for protein. 6360 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: 32.13 Time building geometry restraints manager: 13.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 23219 1.41 - 1.63: 35393 1.63 - 1.85: 648 1.85 - 2.07: 0 2.07 - 2.28: 480 Bond restraints: 59740 Sorted by residual: bond pdb=" C3N NAD B 606 " pdb=" C4N NAD B 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C3N NAD K 606 " pdb=" C4N NAD K 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C3N NAD H 606 " pdb=" C4N NAD H 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C3N NAD E 606 " pdb=" C4N NAD E 606 " ideal model delta sigma weight residual 1.390 1.506 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" O2B NDP L1203 " pdb=" P2B NDP L1203 " ideal model delta sigma weight residual 1.833 1.631 0.202 3.80e-02 6.93e+02 2.81e+01 ... (remaining 59735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 80510 3.79 - 7.59: 510 7.59 - 11.38: 124 11.38 - 15.17: 20 15.17 - 18.96: 16 Bond angle restraints: 81180 Sorted by residual: angle pdb=" C5B NDP I1203 " pdb=" O5B NDP I1203 " pdb=" PA NDP I1203 " ideal model delta sigma weight residual 103.84 122.80 -18.96 1.91e+00 2.73e-01 9.81e+01 angle pdb=" C5B NDP C1203 " pdb=" O5B NDP C1203 " pdb=" PA NDP C1203 " ideal model delta sigma weight residual 103.84 122.80 -18.96 1.91e+00 2.73e-01 9.81e+01 angle pdb=" C5B NDP F1203 " pdb=" O5B NDP F1203 " pdb=" PA NDP F1203 " ideal model delta sigma weight residual 103.84 122.80 -18.96 1.91e+00 2.73e-01 9.81e+01 angle pdb=" C5B NDP L1203 " pdb=" O5B NDP L1203 " pdb=" PA NDP L1203 " ideal model delta sigma weight residual 103.84 122.77 -18.93 1.91e+00 2.73e-01 9.77e+01 angle pdb=" PA NDP L1203 " pdb=" O3 NDP L1203 " pdb=" PN NDP L1203 " ideal model delta sigma weight residual 107.74 125.45 -17.71 1.95e+00 2.62e-01 8.21e+01 ... (remaining 81175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 34933 33.68 - 67.35: 1091 67.35 - 101.03: 100 101.03 - 134.70: 4 134.70 - 168.38: 4 Dihedral angle restraints: 36132 sinusoidal: 14448 harmonic: 21684 Sorted by residual: dihedral pdb=" C10 FMN K 603 " pdb=" C1' FMN K 603 " pdb=" N10 FMN K 603 " pdb=" C2' FMN K 603 " ideal model delta sinusoidal sigma weight residual -102.41 65.97 -168.38 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C10 FMN B 603 " pdb=" C1' FMN B 603 " pdb=" N10 FMN B 603 " pdb=" C2' FMN B 603 " ideal model delta sinusoidal sigma weight residual -102.41 65.93 -168.34 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C10 FMN E 603 " pdb=" C1' FMN E 603 " pdb=" N10 FMN E 603 " pdb=" C2' FMN E 603 " ideal model delta sinusoidal sigma weight residual -102.41 65.92 -168.33 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 36129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 8447 0.084 - 0.169: 837 0.169 - 0.253: 20 0.253 - 0.338: 12 0.338 - 0.422: 4 Chirality restraints: 9320 Sorted by residual: chirality pdb=" C2D NDP L1203 " pdb=" C1D NDP L1203 " pdb=" C3D NDP L1203 " pdb=" O2D NDP L1203 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C2D NDP F1203 " pdb=" C1D NDP F1203 " pdb=" C3D NDP F1203 " pdb=" O2D NDP F1203 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C2D NDP C1203 " pdb=" C1D NDP C1203 " pdb=" C3D NDP C1203 " pdb=" O2D NDP C1203 " both_signs ideal model delta sigma weight residual False -2.71 -2.29 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 9317 not shown) Planarity restraints: 10340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP F1203 " 0.329 2.00e-02 2.50e+03 2.42e-01 7.31e+02 pdb=" C3N NDP F1203 " 0.204 2.00e-02 2.50e+03 pdb=" C4N NDP F1203 " -0.004 2.00e-02 2.50e+03 pdb=" C7N NDP F1203 " -0.234 2.00e-02 2.50e+03 pdb=" N1N NDP F1203 " -0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP L1203 " -0.329 2.00e-02 2.50e+03 2.42e-01 7.31e+02 pdb=" C3N NDP L1203 " -0.204 2.00e-02 2.50e+03 pdb=" C4N NDP L1203 " 0.004 2.00e-02 2.50e+03 pdb=" C7N NDP L1203 " 0.233 2.00e-02 2.50e+03 pdb=" N1N NDP L1203 " 0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP C1203 " -0.329 2.00e-02 2.50e+03 2.42e-01 7.30e+02 pdb=" C3N NDP C1203 " -0.204 2.00e-02 2.50e+03 pdb=" C4N NDP C1203 " 0.004 2.00e-02 2.50e+03 pdb=" C7N NDP C1203 " 0.233 2.00e-02 2.50e+03 pdb=" N1N NDP C1203 " 0.296 2.00e-02 2.50e+03 ... (remaining 10337 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3557 2.73 - 3.27: 55421 3.27 - 3.82: 94267 3.82 - 4.36: 118368 4.36 - 4.90: 203151 Nonbonded interactions: 474764 Sorted by model distance: nonbonded pdb=" O TRP E 318 " pdb=" OH TYR E 327 " model vdw 2.190 3.040 nonbonded pdb=" O TRP B 318 " pdb=" OH TYR B 327 " model vdw 2.191 3.040 nonbonded pdb=" O TRP K 318 " pdb=" OH TYR K 327 " model vdw 2.191 3.040 nonbonded pdb=" O TRP H 318 " pdb=" OH TYR H 327 " model vdw 2.191 3.040 nonbonded pdb=" ND2 ASN F 332 " pdb=" O7N NDP F1203 " model vdw 2.224 3.120 ... (remaining 474759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.850 Check model and map are aligned: 0.350 Set scattering table: 0.400 Process input model: 137.850 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 0.202 59740 Z= 0.435 Angle : 0.899 18.963 81180 Z= 0.453 Chirality : 0.050 0.422 9320 Planarity : 0.010 0.340 10340 Dihedral : 16.084 168.379 22308 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.37 % Favored : 95.32 % Rotamer: Outliers : 0.52 % Allowed : 15.20 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.09), residues: 7600 helix: -0.22 (0.09), residues: 2876 sheet: 0.50 (0.17), residues: 1020 loop : -0.51 (0.10), residues: 3704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L1122 HIS 0.004 0.001 HIS F 96 PHE 0.031 0.002 PHE G 76 TYR 0.026 0.002 TYR F 117 ARG 0.007 0.001 ARG L 427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 624 time to evaluate : 4.855 Fit side-chains REVERT: A 145 MET cc_start: 0.6654 (tpp) cc_final: 0.6066 (tpp) REVERT: C 502 VAL cc_start: 0.8593 (m) cc_final: 0.8320 (t) REVERT: D 145 MET cc_start: 0.6636 (tpp) cc_final: 0.6357 (mmt) REVERT: F 366 GLU cc_start: 0.7566 (tp30) cc_final: 0.7034 (tp30) REVERT: F 502 VAL cc_start: 0.8587 (m) cc_final: 0.8318 (t) REVERT: G 145 MET cc_start: 0.6626 (tpp) cc_final: 0.6333 (mmt) REVERT: I 502 VAL cc_start: 0.8589 (m) cc_final: 0.8321 (t) REVERT: J 145 MET cc_start: 0.6623 (tpp) cc_final: 0.6329 (mmt) REVERT: L 502 VAL cc_start: 0.8597 (m) cc_final: 0.8328 (t) outliers start: 32 outliers final: 11 residues processed: 638 average time/residue: 1.2722 time to fit residues: 1055.0168 Evaluate side-chains 580 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 569 time to evaluate : 4.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 809 THR Chi-restraints excluded: chain F residue 890 VAL Chi-restraints excluded: chain H residue 183 ASP Chi-restraints excluded: chain I residue 809 THR Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain L residue 809 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 30.0000 chunk 576 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 388 optimal weight: 10.0000 chunk 307 optimal weight: 0.8980 chunk 595 optimal weight: 30.0000 chunk 230 optimal weight: 20.0000 chunk 362 optimal weight: 6.9990 chunk 443 optimal weight: 4.9990 chunk 690 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 661 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 734 HIS F 661 GLN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 734 HIS I 661 GLN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 734 HIS K 374 ASN L 661 GLN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 734 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 59740 Z= 0.310 Angle : 0.617 12.698 81180 Z= 0.317 Chirality : 0.047 0.332 9320 Planarity : 0.005 0.057 10340 Dihedral : 8.897 166.938 8708 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.08 % Favored : 95.66 % Rotamer: Outliers : 3.31 % Allowed : 15.72 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7600 helix: 0.37 (0.10), residues: 2924 sheet: 0.46 (0.17), residues: 972 loop : -0.47 (0.10), residues: 3704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C1122 HIS 0.004 0.001 HIS C 96 PHE 0.028 0.002 PHE A 76 TYR 0.028 0.001 TYR L 117 ARG 0.004 0.000 ARG C 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 643 time to evaluate : 4.839 Fit side-chains REVERT: B 135 LYS cc_start: 0.6045 (mmtp) cc_final: 0.5811 (tptt) REVERT: B 417 MET cc_start: 0.6289 (tpp) cc_final: 0.6020 (tpp) REVERT: C 69 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: C 366 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: C 447 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: C 502 VAL cc_start: 0.8607 (m) cc_final: 0.8341 (t) REVERT: C 1090 LYS cc_start: 0.8182 (mppt) cc_final: 0.7981 (tppt) REVERT: E 417 MET cc_start: 0.6308 (tpp) cc_final: 0.6042 (tpp) REVERT: F 69 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: F 447 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: F 502 VAL cc_start: 0.8609 (m) cc_final: 0.8344 (t) REVERT: H 417 MET cc_start: 0.6320 (tpp) cc_final: 0.6004 (tpp) REVERT: I 69 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: I 366 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: I 447 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: I 502 VAL cc_start: 0.8605 (m) cc_final: 0.8342 (t) REVERT: K 417 MET cc_start: 0.6310 (tpp) cc_final: 0.6039 (tpp) REVERT: L 69 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: L 366 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: L 447 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: L 502 VAL cc_start: 0.8608 (m) cc_final: 0.8346 (t) outliers start: 204 outliers final: 70 residues processed: 754 average time/residue: 1.2271 time to fit residues: 1213.1445 Evaluate side-chains 673 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 592 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 447 ASP Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 574 optimal weight: 8.9990 chunk 469 optimal weight: 1.9990 chunk 190 optimal weight: 30.0000 chunk 691 optimal weight: 0.8980 chunk 746 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 685 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 554 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN C 540 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN I 540 ASN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 ASN L 540 ASN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 59740 Z= 0.181 Angle : 0.542 12.257 81180 Z= 0.280 Chirality : 0.044 0.331 9320 Planarity : 0.004 0.050 10340 Dihedral : 8.582 167.612 8694 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.50 % Favored : 96.24 % Rotamer: Outliers : 2.71 % Allowed : 16.97 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.10), residues: 7600 helix: 0.83 (0.10), residues: 2920 sheet: 0.51 (0.17), residues: 972 loop : -0.36 (0.10), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F1122 HIS 0.002 0.001 HIS E 512 PHE 0.024 0.001 PHE D 76 TYR 0.030 0.001 TYR E 47 ARG 0.002 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 647 time to evaluate : 4.885 Fit side-chains REVERT: A 145 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6307 (tpp) REVERT: B 135 LYS cc_start: 0.5951 (mmtp) cc_final: 0.5707 (tptt) REVERT: B 359 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4524 (tmt) REVERT: C 69 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: C 366 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: C 502 VAL cc_start: 0.8561 (m) cc_final: 0.8276 (t) REVERT: C 685 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7318 (mmt) REVERT: C 1162 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7743 (mm-30) REVERT: D 145 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6244 (tpp) REVERT: E 359 MET cc_start: 0.5253 (OUTLIER) cc_final: 0.4589 (tmt) REVERT: F 69 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: F 502 VAL cc_start: 0.8564 (m) cc_final: 0.8282 (t) REVERT: F 685 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.7323 (mmt) REVERT: G 145 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6238 (tpp) REVERT: I 69 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: I 366 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: I 502 VAL cc_start: 0.8559 (m) cc_final: 0.8278 (t) REVERT: I 685 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: J 145 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6235 (tpp) REVERT: K 207 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.4592 (mtp) REVERT: L 69 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: L 366 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: L 502 VAL cc_start: 0.8562 (m) cc_final: 0.8282 (t) REVERT: L 685 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7315 (mmt) outliers start: 167 outliers final: 63 residues processed: 735 average time/residue: 1.2543 time to fit residues: 1205.8057 Evaluate side-chains 664 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 583 time to evaluate : 4.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 831 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 831 SER Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 831 SER Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 207 MET Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 348 GLU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 831 SER Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 20.0000 chunk 519 optimal weight: 3.9990 chunk 358 optimal weight: 0.0770 chunk 76 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 464 optimal weight: 1.9990 chunk 693 optimal weight: 0.0010 chunk 734 optimal weight: 0.0980 chunk 362 optimal weight: 6.9990 chunk 657 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 overall best weight: 1.2348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 540 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN F 540 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN I 540 ASN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN L 540 ASN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 59740 Z= 0.170 Angle : 0.543 14.472 81180 Z= 0.277 Chirality : 0.044 0.339 9320 Planarity : 0.004 0.047 10340 Dihedral : 8.560 169.193 8694 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.17 % Rotamer: Outliers : 3.00 % Allowed : 17.62 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.10), residues: 7600 helix: 1.07 (0.10), residues: 2920 sheet: 0.52 (0.17), residues: 1008 loop : -0.35 (0.10), residues: 3672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F1122 HIS 0.002 0.000 HIS C 275 PHE 0.025 0.001 PHE A 76 TYR 0.024 0.001 TYR L 117 ARG 0.004 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 623 time to evaluate : 5.134 Fit side-chains REVERT: A 145 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.6187 (tpp) REVERT: B 359 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4401 (tmt) REVERT: C 69 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: C 366 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 502 VAL cc_start: 0.8557 (m) cc_final: 0.8260 (t) REVERT: C 644 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (ptp) REVERT: C 685 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7293 (mmt) REVERT: C 927 LYS cc_start: 0.7968 (tmmt) cc_final: 0.7650 (pttm) REVERT: D 145 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6179 (tpp) REVERT: E 359 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4409 (tmt) REVERT: F 69 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: F 502 VAL cc_start: 0.8561 (m) cc_final: 0.8267 (t) REVERT: F 644 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8003 (ptp) REVERT: F 685 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.7296 (mmt) REVERT: F 927 LYS cc_start: 0.7980 (tmmt) cc_final: 0.7666 (pttm) REVERT: G 145 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6178 (tpp) REVERT: H 207 MET cc_start: 0.4839 (OUTLIER) cc_final: 0.4152 (mtp) REVERT: I 69 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: I 366 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: I 502 VAL cc_start: 0.8554 (m) cc_final: 0.8260 (t) REVERT: I 644 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8002 (ptp) REVERT: I 685 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.7298 (mmt) REVERT: J 145 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6141 (tpp) REVERT: L 69 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: L 366 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: L 502 VAL cc_start: 0.8557 (m) cc_final: 0.8267 (t) REVERT: L 644 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8000 (ptp) REVERT: L 685 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.7286 (mmt) outliers start: 185 outliers final: 88 residues processed: 733 average time/residue: 1.2247 time to fit residues: 1177.9812 Evaluate side-chains 706 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 596 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 644 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 799 LEU Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1029 MET Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 528 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 644 MET Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 644 MET Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 799 LEU Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 546 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 626 optimal weight: 30.0000 chunk 507 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 375 optimal weight: 0.3980 chunk 659 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 overall best weight: 3.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 540 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 GLN C 719 ASN F 540 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 GLN F 719 ASN I 540 ASN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 680 GLN I 719 ASN L 540 ASN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN L 719 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 59740 Z= 0.309 Angle : 0.602 12.683 81180 Z= 0.307 Chirality : 0.046 0.344 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.719 167.179 8694 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.37 % Favored : 95.47 % Rotamer: Outliers : 3.94 % Allowed : 17.38 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 7600 helix: 0.97 (0.10), residues: 2936 sheet: 0.43 (0.17), residues: 1008 loop : -0.42 (0.10), residues: 3656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L1122 HIS 0.004 0.001 HIS F 149 PHE 0.028 0.002 PHE J 76 TYR 0.025 0.001 TYR E 47 ARG 0.009 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 614 time to evaluate : 4.869 Fit side-chains REVERT: A 50 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7610 (p90) REVERT: A 145 MET cc_start: 0.6597 (mmt) cc_final: 0.6284 (tpp) REVERT: B 359 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4510 (tmt) REVERT: C 69 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: C 366 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: C 502 VAL cc_start: 0.8693 (m) cc_final: 0.8418 (t) REVERT: C 685 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.7313 (mmt) REVERT: D 50 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7690 (p90) REVERT: D 145 MET cc_start: 0.6593 (mmt) cc_final: 0.6307 (tpp) REVERT: E 359 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.4619 (tmt) REVERT: F 69 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: F 502 VAL cc_start: 0.8697 (m) cc_final: 0.8423 (t) REVERT: F 685 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: G 50 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7687 (p90) REVERT: G 145 MET cc_start: 0.6594 (mmt) cc_final: 0.6305 (tpp) REVERT: I 69 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: I 366 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: I 502 VAL cc_start: 0.8692 (m) cc_final: 0.8418 (t) REVERT: I 685 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.7309 (mmt) REVERT: J 50 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7694 (p90) REVERT: J 145 MET cc_start: 0.6581 (mmt) cc_final: 0.6293 (tpp) REVERT: L 69 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: L 366 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: L 502 VAL cc_start: 0.8695 (m) cc_final: 0.8424 (t) REVERT: L 685 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.7311 (mmt) outliers start: 243 outliers final: 119 residues processed: 766 average time/residue: 1.2040 time to fit residues: 1221.1928 Evaluate side-chains 729 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 593 time to evaluate : 4.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 359 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 528 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 681 ILE Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain J residue 50 TYR Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 681 ILE Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 9.9990 chunk 661 optimal weight: 0.0050 chunk 145 optimal weight: 1.9990 chunk 431 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 735 optimal weight: 8.9990 chunk 610 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 chunk 386 optimal weight: 0.9980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN H 382 GLN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 59740 Z= 0.193 Angle : 0.559 13.618 81180 Z= 0.285 Chirality : 0.044 0.345 9320 Planarity : 0.004 0.051 10340 Dihedral : 8.316 168.201 8692 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.07 % Rotamer: Outliers : 3.00 % Allowed : 18.38 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7600 helix: 1.12 (0.10), residues: 2924 sheet: 0.41 (0.17), residues: 1008 loop : -0.38 (0.10), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L1122 HIS 0.002 0.001 HIS L 96 PHE 0.026 0.001 PHE D 76 TYR 0.024 0.001 TYR C 117 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 625 time to evaluate : 4.802 Fit side-chains REVERT: C 69 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: C 105 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8297 (ttt) REVERT: C 366 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: C 502 VAL cc_start: 0.8668 (m) cc_final: 0.8400 (t) REVERT: C 685 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7366 (mmt) REVERT: D 145 MET cc_start: 0.6650 (mmt) cc_final: 0.6345 (tpp) REVERT: F 69 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: F 105 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8290 (ttt) REVERT: F 502 VAL cc_start: 0.8669 (m) cc_final: 0.8403 (t) REVERT: F 534 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6992 (tm-30) REVERT: F 685 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7370 (mmt) REVERT: G 145 MET cc_start: 0.6609 (mmt) cc_final: 0.6334 (tpp) REVERT: I 69 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: I 105 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8295 (ttt) REVERT: I 366 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: I 502 VAL cc_start: 0.8663 (m) cc_final: 0.8398 (t) REVERT: I 685 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7355 (mmt) REVERT: J 145 MET cc_start: 0.6633 (mmt) cc_final: 0.6326 (tpp) REVERT: L 69 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: L 105 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8298 (ttt) REVERT: L 366 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: L 502 VAL cc_start: 0.8669 (m) cc_final: 0.8404 (t) REVERT: L 685 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7366 (mmt) outliers start: 185 outliers final: 115 residues processed: 738 average time/residue: 1.1950 time to fit residues: 1162.8653 Evaluate side-chains 714 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 584 time to evaluate : 4.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 799 LEU Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 360 SER Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 528 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 1001 LEU Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 360 SER Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 348 GLU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 1001 LEU Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 418 optimal weight: 20.0000 chunk 536 optimal weight: 7.9990 chunk 416 optimal weight: 8.9990 chunk 618 optimal weight: 0.0040 chunk 410 optimal weight: 20.0000 chunk 732 optimal weight: 5.9990 chunk 458 optimal weight: 0.0770 chunk 446 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 overall best weight: 2.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN C 540 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN E 382 GLN ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN H 382 GLN I 540 ASN ** I 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN K 382 GLN L 540 ASN ** L 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 59740 Z= 0.241 Angle : 0.578 12.547 81180 Z= 0.295 Chirality : 0.045 0.345 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.087 167.307 8692 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.28 % Favored : 95.57 % Rotamer: Outliers : 3.49 % Allowed : 18.59 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7600 helix: 1.13 (0.10), residues: 2920 sheet: 0.36 (0.17), residues: 1008 loop : -0.37 (0.10), residues: 3672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L1122 HIS 0.004 0.001 HIS C 149 PHE 0.028 0.001 PHE D 76 TYR 0.023 0.001 TYR I 117 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 601 time to evaluate : 5.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.1914 (p90) cc_final: 0.1336 (m-10) REVERT: C 69 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: C 105 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8379 (ttt) REVERT: C 187 MET cc_start: 0.8152 (mtp) cc_final: 0.7848 (mtm) REVERT: C 366 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: C 502 VAL cc_start: 0.8742 (m) cc_final: 0.8483 (t) REVERT: C 685 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: E 62 TYR cc_start: 0.2064 (p90) cc_final: 0.1416 (m-10) REVERT: F 69 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: F 105 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8376 (ttt) REVERT: F 187 MET cc_start: 0.8149 (mtp) cc_final: 0.7861 (mtm) REVERT: F 502 VAL cc_start: 0.8733 (m) cc_final: 0.8474 (t) REVERT: F 644 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7991 (ptp) REVERT: F 685 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7301 (mmt) REVERT: H 62 TYR cc_start: 0.1971 (p90) cc_final: 0.1366 (m-10) REVERT: I 69 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: I 105 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8380 (ttt) REVERT: I 366 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: I 447 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: I 502 VAL cc_start: 0.8736 (m) cc_final: 0.8482 (t) REVERT: I 685 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7313 (mmt) REVERT: K 62 TYR cc_start: 0.2005 (p90) cc_final: 0.1379 (m-10) REVERT: L 69 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: L 105 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8383 (ttt) REVERT: L 366 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: L 502 VAL cc_start: 0.8745 (m) cc_final: 0.8491 (t) REVERT: L 644 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7988 (ptp) REVERT: L 685 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7308 (mmt) outliers start: 215 outliers final: 130 residues processed: 745 average time/residue: 1.1702 time to fit residues: 1161.4630 Evaluate side-chains 738 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 590 time to evaluate : 4.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 644 MET Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 799 LEU Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 528 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 447 ASP Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 348 GLU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 644 MET Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 799 LEU Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 0.6980 chunk 292 optimal weight: 10.0000 chunk 437 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 465 optimal weight: 1.9990 chunk 499 optimal weight: 7.9990 chunk 362 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 575 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN C 680 GLN C 719 ASN E 382 GLN F 680 GLN F 719 ASN H 382 GLN I 680 GLN I 719 ASN K 382 GLN L 680 GLN L 719 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 59740 Z= 0.251 Angle : 0.585 13.353 81180 Z= 0.298 Chirality : 0.045 0.348 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.016 167.069 8692 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 3.50 % Allowed : 18.79 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.10), residues: 7600 helix: 1.12 (0.10), residues: 2920 sheet: 0.33 (0.17), residues: 1008 loop : -0.36 (0.10), residues: 3672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I1122 HIS 0.003 0.001 HIS I 149 PHE 0.028 0.001 PHE D 76 TYR 0.023 0.001 TYR L 117 ARG 0.004 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 605 time to evaluate : 5.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.2144 (p90) cc_final: 0.1493 (m-10) REVERT: B 420 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7293 (mpt) REVERT: C 69 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: C 105 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: C 187 MET cc_start: 0.8231 (mtp) cc_final: 0.7993 (mtm) REVERT: C 366 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: C 502 VAL cc_start: 0.8767 (m) cc_final: 0.8516 (t) REVERT: C 534 GLU cc_start: 0.7225 (mm-30) cc_final: 0.7022 (tm-30) REVERT: C 685 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7354 (mmt) REVERT: E 62 TYR cc_start: 0.2277 (p90) cc_final: 0.1569 (m-10) REVERT: F 69 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: F 105 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: F 187 MET cc_start: 0.8239 (mtp) cc_final: 0.7981 (mtm) REVERT: F 447 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: F 502 VAL cc_start: 0.8770 (m) cc_final: 0.8521 (t) REVERT: F 685 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7322 (mmt) REVERT: F 721 ASP cc_start: 0.7936 (m-30) cc_final: 0.7728 (m-30) REVERT: H 62 TYR cc_start: 0.2252 (p90) cc_final: 0.1567 (m-10) REVERT: I 69 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: I 105 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8380 (ttt) REVERT: I 366 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: I 502 VAL cc_start: 0.8763 (m) cc_final: 0.8516 (t) REVERT: I 685 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.7351 (mmt) REVERT: I 721 ASP cc_start: 0.7940 (m-30) cc_final: 0.7734 (m-30) REVERT: K 62 TYR cc_start: 0.2280 (p90) cc_final: 0.1578 (m-10) REVERT: L 69 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: L 105 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8380 (ttt) REVERT: L 366 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: L 447 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: L 502 VAL cc_start: 0.8766 (m) cc_final: 0.8519 (t) REVERT: L 685 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7313 (mmt) REVERT: L 721 ASP cc_start: 0.7933 (m-30) cc_final: 0.7730 (m-30) outliers start: 216 outliers final: 143 residues processed: 755 average time/residue: 1.1958 time to fit residues: 1198.3834 Evaluate side-chains 756 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 595 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 507 ASP Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain F residue 799 LEU Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 1001 LEU Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain H residue 528 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 507 ASP Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 348 GLU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 799 LEU Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 3.9990 chunk 701 optimal weight: 0.4980 chunk 640 optimal weight: 3.9990 chunk 682 optimal weight: 9.9990 chunk 410 optimal weight: 0.0980 chunk 297 optimal weight: 7.9990 chunk 536 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 616 optimal weight: 3.9990 chunk 645 optimal weight: 2.9990 chunk 680 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN E 382 GLN F 680 GLN F 719 ASN H 382 GLN ** I 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 ASN K 382 GLN L 680 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 59740 Z= 0.207 Angle : 0.573 13.870 81180 Z= 0.293 Chirality : 0.044 0.342 9320 Planarity : 0.004 0.049 10340 Dihedral : 7.984 167.983 8692 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.22 % Favored : 95.62 % Rotamer: Outliers : 2.90 % Allowed : 19.45 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 7600 helix: 1.17 (0.10), residues: 2924 sheet: 0.32 (0.17), residues: 1008 loop : -0.34 (0.11), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L1122 HIS 0.003 0.001 HIS F 149 PHE 0.026 0.001 PHE G 76 TYR 0.024 0.001 TYR F 117 ARG 0.004 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 615 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2761 (OUTLIER) cc_final: 0.1212 (mtm) REVERT: B 62 TYR cc_start: 0.2160 (p90) cc_final: 0.1466 (m-10) REVERT: B 420 MET cc_start: 0.7494 (mpt) cc_final: 0.7265 (mpt) REVERT: B 528 THR cc_start: 0.3445 (OUTLIER) cc_final: 0.2795 (m) REVERT: C 69 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: C 105 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8379 (ttt) REVERT: C 366 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: C 502 VAL cc_start: 0.8747 (m) cc_final: 0.8498 (t) REVERT: C 685 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7327 (mmt) REVERT: E 62 TYR cc_start: 0.2390 (p90) cc_final: 0.1646 (m-10) REVERT: E 320 MET cc_start: 0.2720 (mmm) cc_final: 0.2500 (mmm) REVERT: E 528 THR cc_start: 0.3427 (OUTLIER) cc_final: 0.2802 (m) REVERT: F 69 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: F 105 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8352 (ttt) REVERT: F 447 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: F 502 VAL cc_start: 0.8740 (m) cc_final: 0.8491 (t) REVERT: F 685 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7355 (mmt) REVERT: H 62 TYR cc_start: 0.2426 (p90) cc_final: 0.1614 (m-10) REVERT: H 528 THR cc_start: 0.3383 (OUTLIER) cc_final: 0.2745 (m) REVERT: I 69 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: I 105 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8351 (ttt) REVERT: I 366 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: I 502 VAL cc_start: 0.8721 (m) cc_final: 0.8471 (t) REVERT: I 685 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7363 (mmt) REVERT: K 62 TYR cc_start: 0.2421 (p90) cc_final: 0.1606 (m-10) REVERT: L 69 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: L 105 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8353 (ttt) REVERT: L 366 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: L 502 VAL cc_start: 0.8723 (m) cc_final: 0.8473 (t) REVERT: L 685 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7338 (mmt) outliers start: 179 outliers final: 138 residues processed: 734 average time/residue: 1.1948 time to fit residues: 1167.0891 Evaluate side-chains 760 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 602 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 507 ASP Chi-restraints excluded: chain E residue 528 THR Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 799 LEU Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1053 THR Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain F residue 1149 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 507 ASP Chi-restraints excluded: chain H residue 528 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1053 THR Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 207 MET Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 387 SER Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 507 ASP Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 799 LEU Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1053 THR Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 40.0000 chunk 721 optimal weight: 0.9980 chunk 440 optimal weight: 5.9990 chunk 342 optimal weight: 0.9980 chunk 501 optimal weight: 0.9990 chunk 757 optimal weight: 6.9990 chunk 696 optimal weight: 6.9990 chunk 602 optimal weight: 0.0010 chunk 62 optimal weight: 5.9990 chunk 465 optimal weight: 1.9990 chunk 369 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN F 540 ASN H 382 GLN I 540 ASN ** I 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN L 540 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 59740 Z= 0.163 Angle : 0.566 13.003 81180 Z= 0.288 Chirality : 0.043 0.330 9320 Planarity : 0.004 0.050 10340 Dihedral : 7.967 169.680 8692 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.71 % Favored : 96.13 % Rotamer: Outliers : 2.51 % Allowed : 20.05 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 7600 helix: 1.21 (0.10), residues: 2952 sheet: 0.32 (0.17), residues: 1008 loop : -0.27 (0.11), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L1122 HIS 0.002 0.000 HIS L 734 PHE 0.024 0.001 PHE D 76 TYR 0.024 0.001 TYR F 117 ARG 0.004 0.000 ARG H 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15200 Ramachandran restraints generated. 7600 Oldfield, 0 Emsley, 7600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 639 time to evaluate : 4.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.7073 (mmt) cc_final: 0.6747 (mmp) REVERT: B 62 TYR cc_start: 0.2209 (p90) cc_final: 0.1546 (m-10) REVERT: B 420 MET cc_start: 0.7455 (mpt) cc_final: 0.7218 (mpt) REVERT: C 69 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: C 105 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8321 (ttt) REVERT: C 366 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: C 502 VAL cc_start: 0.8677 (m) cc_final: 0.8415 (t) REVERT: C 685 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7368 (mmt) REVERT: C 927 LYS cc_start: 0.7866 (tmmt) cc_final: 0.7584 (pttm) REVERT: E 18 LYS cc_start: 0.4886 (mttt) cc_final: 0.4623 (mmmm) REVERT: E 62 TYR cc_start: 0.2596 (p90) cc_final: 0.1770 (m-10) REVERT: E 320 MET cc_start: 0.2828 (mmm) cc_final: 0.2532 (mmm) REVERT: F 69 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: F 105 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8332 (ttt) REVERT: F 502 VAL cc_start: 0.8678 (m) cc_final: 0.8416 (t) REVERT: F 644 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7884 (mtp) REVERT: F 685 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7359 (mmt) REVERT: F 927 LYS cc_start: 0.7869 (tmmt) cc_final: 0.7584 (pttm) REVERT: H 18 LYS cc_start: 0.4890 (mttt) cc_final: 0.4623 (mmmm) REVERT: H 62 TYR cc_start: 0.2633 (p90) cc_final: 0.1833 (m-10) REVERT: I 69 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: I 105 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8320 (ttt) REVERT: I 366 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: I 502 VAL cc_start: 0.8666 (m) cc_final: 0.8403 (t) REVERT: I 644 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7986 (ptp) REVERT: I 685 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7380 (mmt) REVERT: I 927 LYS cc_start: 0.7871 (tmmt) cc_final: 0.7589 (pttm) REVERT: K 18 LYS cc_start: 0.4886 (mttt) cc_final: 0.4631 (mmmm) REVERT: K 62 TYR cc_start: 0.2596 (p90) cc_final: 0.1777 (m-10) REVERT: K 528 THR cc_start: 0.3324 (OUTLIER) cc_final: 0.2741 (m) REVERT: L 69 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: L 105 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8321 (ttt) REVERT: L 366 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: L 502 VAL cc_start: 0.8670 (m) cc_final: 0.8408 (t) REVERT: L 685 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7361 (mmt) REVERT: L 927 LYS cc_start: 0.7916 (tmmt) cc_final: 0.7601 (pttm) outliers start: 155 outliers final: 120 residues processed: 740 average time/residue: 1.1936 time to fit residues: 1175.6691 Evaluate side-chains 753 residues out of total 6164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 615 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 507 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 644 MET Chi-restraints excluded: chain F residue 671 CYS Chi-restraints excluded: chain F residue 676 VAL Chi-restraints excluded: chain F residue 685 MET Chi-restraints excluded: chain F residue 695 CYS Chi-restraints excluded: chain F residue 799 LEU Chi-restraints excluded: chain F residue 968 VAL Chi-restraints excluded: chain F residue 1025 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 396 LEU Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 348 GLU Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 375 VAL Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain I residue 549 THR Chi-restraints excluded: chain I residue 644 MET Chi-restraints excluded: chain I residue 671 CYS Chi-restraints excluded: chain I residue 676 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 695 CYS Chi-restraints excluded: chain I residue 799 LEU Chi-restraints excluded: chain I residue 968 VAL Chi-restraints excluded: chain I residue 1025 VAL Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain I residue 1149 VAL Chi-restraints excluded: chain K residue 48 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 274 GLU Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 446 ILE Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 507 ASP Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 366 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 495 SER Chi-restraints excluded: chain L residue 516 THR Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 549 THR Chi-restraints excluded: chain L residue 676 VAL Chi-restraints excluded: chain L residue 685 MET Chi-restraints excluded: chain L residue 695 CYS Chi-restraints excluded: chain L residue 799 LEU Chi-restraints excluded: chain L residue 968 VAL Chi-restraints excluded: chain L residue 1025 VAL Chi-restraints excluded: chain L residue 1136 THR Chi-restraints excluded: chain L residue 1149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 1.9990 chunk 642 optimal weight: 30.0000 chunk 184 optimal weight: 9.9990 chunk 555 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 603 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 620 optimal weight: 30.0000 chunk 76 optimal weight: 0.0270 chunk 111 optimal weight: 9.9990 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN C 540 ASN ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN H 382 GLN ** I 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141772 restraints weight = 62394.643| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.02 r_work: 0.3094 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 59740 Z= 0.274 Angle : 0.617 14.341 81180 Z= 0.313 Chirality : 0.046 0.356 9320 Planarity : 0.004 0.049 10340 Dihedral : 8.099 167.949 8692 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 2.77 % Allowed : 20.20 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 7600 helix: 1.15 (0.10), residues: 2928 sheet: 0.27 (0.17), residues: 1008 loop : -0.30 (0.11), residues: 3664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L1122 HIS 0.004 0.001 HIS I 149 PHE 0.029 0.001 PHE G 76 TYR 0.022 0.001 TYR L 117 ARG 0.006 0.000 ARG J 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17255.40 seconds wall clock time: 300 minutes 6.65 seconds (18006.65 seconds total)