Starting phenix.real_space_refine on Thu Feb 22 04:06:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe9_13349/02_2024/7pe9_13349_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe9_13349/02_2024/7pe9_13349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe9_13349/02_2024/7pe9_13349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe9_13349/02_2024/7pe9_13349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe9_13349/02_2024/7pe9_13349_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe9_13349/02_2024/7pe9_13349_updated.pdb" } resolution = 3.7 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= -0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1785 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 S 186 5.16 5 C 19661 2.51 5 N 5536 2.21 5 O 5686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31076 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2194, 16419 Classifications: {'peptide': 2194} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 88, 'TRANS': 2105} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1672 Unresolved non-hydrogen dihedrals: 1079 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 33, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 714 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8917 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2580 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26955 SG CYS E1520 24.339 72.610 159.100 1.00150.21 S ATOM 26981 SG CYS E1523 20.620 72.811 159.184 1.00152.50 S ATOM 27441 SG CYS E1651 22.439 75.846 157.870 1.00135.63 S Time building chain proxies: 14.99, per 1000 atoms: 0.48 Number of scatterers: 31076 At special positions: 0 Unit cell: (152.352, 155.526, 204.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 186 16.00 P 6 15.00 O 5686 8.00 N 5536 7.00 C 19661 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.11 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E4801 " pdb="ZN ZN E4801 " - pdb=" NE2 HIS E1515 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1523 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1520 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1651 " Number of angles added : 3 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 208 helices and 18 sheets defined 58.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.95 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.510A pdb=" N ARG A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.583A pdb=" N PHE A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.891A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 363 through 375 Processing helix chain 'A' and resid 387 through 402 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 452 through 465 removed outlier: 3.959A pdb=" N ALA A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.509A pdb=" N LEU A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 581 through 591 removed outlier: 3.867A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 607 removed outlier: 3.548A pdb=" N HIS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 616 through 628 removed outlier: 3.521A pdb=" N GLU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 3.549A pdb=" N SER A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.578A pdb=" N CYS A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 685 removed outlier: 4.488A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.780A pdb=" N ALA A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 removed outlier: 3.674A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 717 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 removed outlier: 3.789A pdb=" N MET A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 747 through 763 Processing helix chain 'A' and resid 765 through 783 Proline residue: A 770 - end of helix removed outlier: 6.011A pdb=" N GLU A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Proline residue: A 774 - end of helix removed outlier: 3.599A pdb=" N LYS A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 808 removed outlier: 3.693A pdb=" N ASN A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 828 removed outlier: 4.404A pdb=" N ILE A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 856 through 860 removed outlier: 3.921A pdb=" N LYS A 860 " --> pdb=" O PRO A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 874 removed outlier: 3.733A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 891 removed outlier: 3.605A pdb=" N ILE A 885 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 930 through 936 removed outlier: 3.719A pdb=" N VAL A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 959 removed outlier: 4.025A pdb=" N TYR A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Proline residue: A 948 - end of helix removed outlier: 3.525A pdb=" N VAL A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 982 removed outlier: 3.898A pdb=" N THR A 969 " --> pdb=" O HIS A 966 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 971 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 972 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 976 " --> pdb=" O GLN A 973 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A 979 " --> pdb=" O THR A 976 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 982 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1003 Proline residue: A 991 - end of helix removed outlier: 4.945A pdb=" N MET A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 3.871A pdb=" N LEU A 998 " --> pdb=" O PRO A 995 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1022 removed outlier: 3.996A pdb=" N GLN A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1040 removed outlier: 4.431A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1063 Processing helix chain 'A' and resid 1067 through 1081 removed outlier: 3.747A pdb=" N LEU A1071 " --> pdb=" O LYS A1068 " (cutoff:3.500A) Proline residue: A1072 - end of helix Proline residue: A1076 - end of helix removed outlier: 3.637A pdb=" N LEU A1079 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A1080 " --> pdb=" O HIS A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.940A pdb=" N ILE A1091 " --> pdb=" O PRO A1088 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL A1092 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A1098 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1119 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.862A pdb=" N VAL A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1142 " --> pdb=" O THR A1138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1163 removed outlier: 3.932A pdb=" N HIS A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.927A pdb=" N ASP A1175 " --> pdb=" O SER A1171 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1202 removed outlier: 3.922A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Proline residue: A1193 - end of helix removed outlier: 3.738A pdb=" N ASN A1196 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS A1197 " --> pdb=" O MET A1194 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A1200 " --> pdb=" O LYS A1197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A1201 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A1202 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1217 removed outlier: 3.505A pdb=" N VAL A1211 " --> pdb=" O GLN A1207 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1237 Processing helix chain 'A' and resid 1265 through 1269 Processing helix chain 'A' and resid 1277 through 1293 Processing helix chain 'A' and resid 1298 through 1309 removed outlier: 4.163A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1315 No H-bonds generated for 'chain 'A' and resid 1312 through 1315' Processing helix chain 'A' and resid 1318 through 1328 removed outlier: 3.521A pdb=" N SER A1324 " --> pdb=" O ALA A1320 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1345 removed outlier: 3.619A pdb=" N GLU A1336 " --> pdb=" O ASP A1332 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A1337 " --> pdb=" O GLN A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1366 Processing helix chain 'A' and resid 1377 through 1388 removed outlier: 3.525A pdb=" N ILE A1380 " --> pdb=" O ASP A1377 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A1381 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A1383 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A1384 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1387 " --> pdb=" O GLY A1384 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A1388 " --> pdb=" O GLU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1406 removed outlier: 3.724A pdb=" N LYS A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1423 Processing helix chain 'A' and resid 1426 through 1438 removed outlier: 3.550A pdb=" N VAL A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.804A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1453 " --> pdb=" O TRP A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1468 removed outlier: 3.540A pdb=" N VAL A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1487 removed outlier: 3.531A pdb=" N MET A1481 " --> pdb=" O MET A1477 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1486 " --> pdb=" O ARG A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1501 removed outlier: 3.763A pdb=" N GLN A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1523 removed outlier: 3.685A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 3.929A pdb=" N GLU A1530 " --> pdb=" O TRP A1526 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A1534 " --> pdb=" O GLU A1530 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 removed outlier: 4.289A pdb=" N ARG A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1550 " --> pdb=" O TYR A1546 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A1553 " --> pdb=" O VAL A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1580 removed outlier: 3.841A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A1569 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1570 " --> pdb=" O LYS A1566 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1587 No H-bonds generated for 'chain 'A' and resid 1585 through 1587' Processing helix chain 'A' and resid 1590 through 1607 removed outlier: 3.838A pdb=" N GLU A1600 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1601 " --> pdb=" O SER A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1615 through 1623 removed outlier: 5.427A pdb=" N TRP A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A1621 " --> pdb=" O GLN A1617 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1623 " --> pdb=" O TRP A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1641 removed outlier: 3.520A pdb=" N MET A1638 " --> pdb=" O GLN A1634 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A1641 " --> pdb=" O LEU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1648 No H-bonds generated for 'chain 'A' and resid 1646 through 1648' Processing helix chain 'A' and resid 1650 through 1663 removed outlier: 4.115A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1677 removed outlier: 3.854A pdb=" N LEU A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A1676 " --> pdb=" O THR A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1706 Processing helix chain 'A' and resid 1710 through 1728 removed outlier: 3.540A pdb=" N GLN A1715 " --> pdb=" O ILE A1711 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A1725 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1762 removed outlier: 3.574A pdb=" N ALA A1748 " --> pdb=" O HIS A1744 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1766 through 1782 Proline residue: A1770 - end of helix removed outlier: 3.591A pdb=" N GLU A1781 " --> pdb=" O SER A1777 " (cutoff:3.500A) Processing helix chain 'A' and resid 1787 through 1808 removed outlier: 3.721A pdb=" N ALA A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1895 removed outlier: 3.565A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix Processing helix chain 'A' and resid 1900 through 1913 removed outlier: 4.109A pdb=" N LEU A1907 " --> pdb=" O THR A1903 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A1908 " --> pdb=" O LEU A1904 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1909 " --> pdb=" O ARG A1905 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1929 removed outlier: 3.975A pdb=" N GLU A1921 " --> pdb=" O PRO A1917 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A1925 " --> pdb=" O GLU A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1939 through 1945 removed outlier: 3.976A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1967 removed outlier: 4.677A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A1957 " --> pdb=" O VAL A1953 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A1958 " --> pdb=" O GLY A1954 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A1960 " --> pdb=" O LEU A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1973 through 1980 Processing helix chain 'A' and resid 1985 through 2001 removed outlier: 3.544A pdb=" N ILE A1994 " --> pdb=" O ALA A1990 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2020 removed outlier: 3.508A pdb=" N GLN A2007 " --> pdb=" O ASN A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2023 through 2040 Processing helix chain 'A' and resid 2045 through 2056 removed outlier: 3.796A pdb=" N GLU A2049 " --> pdb=" O LYS A2045 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A2050 " --> pdb=" O GLY A2046 " (cutoff:3.500A) Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2065 through 2073 Processing helix chain 'A' and resid 2075 through 2091 removed outlier: 3.568A pdb=" N GLU A2083 " --> pdb=" O MET A2079 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2112 removed outlier: 4.027A pdb=" N LEU A2103 " --> pdb=" O GLN A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2126 No H-bonds generated for 'chain 'A' and resid 2123 through 2126' Processing helix chain 'A' and resid 2193 through 2210 removed outlier: 3.708A pdb=" N ARG A2197 " --> pdb=" O ARG A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2213 through 2216 No H-bonds generated for 'chain 'A' and resid 2213 through 2216' Processing helix chain 'A' and resid 2246 through 2256 removed outlier: 3.584A pdb=" N TYR A2253 " --> pdb=" O LEU A2249 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2271 Processing helix chain 'A' and resid 2275 through 2277 No H-bonds generated for 'chain 'A' and resid 2275 through 2277' Processing helix chain 'A' and resid 2280 through 2293 removed outlier: 3.604A pdb=" N GLU A2285 " --> pdb=" O MET A2281 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A2292 " --> pdb=" O GLU A2288 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2305 removed outlier: 3.851A pdb=" N TRP A2304 " --> pdb=" O ALA A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2334 removed outlier: 3.919A pdb=" N VAL A2326 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A2327 " --> pdb=" O SER A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2341 through 2343 No H-bonds generated for 'chain 'A' and resid 2341 through 2343' Processing helix chain 'A' and resid 2364 through 2367 No H-bonds generated for 'chain 'A' and resid 2364 through 2367' Processing helix chain 'A' and resid 2381 through 2384 No H-bonds generated for 'chain 'A' and resid 2381 through 2384' Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2411 through 2422 removed outlier: 3.746A pdb=" N VAL A2417 " --> pdb=" O SER A2413 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2431 No H-bonds generated for 'chain 'A' and resid 2429 through 2431' Processing helix chain 'A' and resid 2493 through 2507 removed outlier: 4.407A pdb=" N LYS A2496 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A2502 " --> pdb=" O GLN A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2521 through 2532 Processing helix chain 'A' and resid 2535 through 2539 Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'E' and resid 33 through 42 removed outlier: 4.016A pdb=" N ARG E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 53 through 69 Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.536A pdb=" N ILE E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 133 removed outlier: 3.532A pdb=" N ILE E 129 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA E 130 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 156 removed outlier: 3.652A pdb=" N GLN E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 163 through 174 removed outlier: 3.507A pdb=" N SER E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 197 removed outlier: 3.675A pdb=" N ALA E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 207 through 216 removed outlier: 3.787A pdb=" N ILE E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 234 removed outlier: 3.515A pdb=" N ILE E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 250 through 258 removed outlier: 3.564A pdb=" N ILE E 253 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 273 through 292 removed outlier: 3.517A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 301 removed outlier: 3.660A pdb=" N ILE E 299 " --> pdb=" O TRP E 295 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.799A pdb=" N LEU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 334 removed outlier: 3.533A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 387 through 402 removed outlier: 3.716A pdb=" N TYR E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 417 through 434 removed outlier: 3.895A pdb=" N VAL E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 426 " --> pdb=" O ARG E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 450 through 457 Processing helix chain 'E' and resid 463 through 485 removed outlier: 3.573A pdb=" N LEU E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE E 479 " --> pdb=" O CYS E 475 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU E 481 " --> pdb=" O LYS E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 506 removed outlier: 3.581A pdb=" N ILE E 497 " --> pdb=" O HIS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 535 Processing helix chain 'E' and resid 548 through 555 removed outlier: 3.863A pdb=" N GLY E 552 " --> pdb=" O TRP E 548 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 553 " --> pdb=" O ASN E 549 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 581 removed outlier: 3.803A pdb=" N PHE E 580 " --> pdb=" O ARG E 576 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 614 removed outlier: 3.686A pdb=" N PHE E 611 " --> pdb=" O GLN E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 637 removed outlier: 3.938A pdb=" N ASP E 625 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 626 " --> pdb=" O TYR E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 651 removed outlier: 3.647A pdb=" N LEU E 651 " --> pdb=" O ASN E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 657 No H-bonds generated for 'chain 'E' and resid 655 through 657' Processing helix chain 'E' and resid 660 through 664 Processing helix chain 'E' and resid 670 through 679 removed outlier: 3.653A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET E 675 " --> pdb=" O HIS E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 689 removed outlier: 3.781A pdb=" N CYS E 689 " --> pdb=" O LEU E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 696 through 704 removed outlier: 3.568A pdb=" N SER E 703 " --> pdb=" O LYS E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 Processing helix chain 'E' and resid 726 through 736 removed outlier: 3.608A pdb=" N TYR E 731 " --> pdb=" O ALA E 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 741 No H-bonds generated for 'chain 'E' and resid 738 through 741' Processing helix chain 'E' and resid 747 through 750 No H-bonds generated for 'chain 'E' and resid 747 through 750' Processing helix chain 'E' and resid 752 through 760 removed outlier: 3.760A pdb=" N THR E 757 " --> pdb=" O GLU E 753 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN E 758 " --> pdb=" O LEU E 754 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 759 " --> pdb=" O LEU E 755 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS E 760 " --> pdb=" O VAL E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 779 removed outlier: 3.514A pdb=" N ASP E 772 " --> pdb=" O SER E 768 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 777 " --> pdb=" O ILE E 773 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 790 Processing helix chain 'E' and resid 799 through 810 removed outlier: 3.811A pdb=" N ARG E 807 " --> pdb=" O LEU E 803 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE E 808 " --> pdb=" O LEU E 804 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU E 809 " --> pdb=" O LEU E 805 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER E 810 " --> pdb=" O LEU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 818 removed outlier: 3.553A pdb=" N TYR E 817 " --> pdb=" O LYS E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 830 removed outlier: 3.588A pdb=" N GLU E 829 " --> pdb=" O ALA E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 838 through 850 Processing helix chain 'E' and resid 882 through 885 No H-bonds generated for 'chain 'E' and resid 882 through 885' Processing helix chain 'E' and resid 890 through 898 removed outlier: 3.671A pdb=" N LEU E 895 " --> pdb=" O THR E 891 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 896 " --> pdb=" O GLY E 892 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 897 " --> pdb=" O CYS E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 910 removed outlier: 3.509A pdb=" N ASN E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 909 " --> pdb=" O LEU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 917 through 935 removed outlier: 3.976A pdb=" N LYS E 921 " --> pdb=" O TRP E 917 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 923 " --> pdb=" O GLU E 919 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA E 929 " --> pdb=" O ALA E 925 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN E 932 " --> pdb=" O TRP E 928 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 933 " --> pdb=" O ALA E 929 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER E 935 " --> pdb=" O GLY E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 940 No H-bonds generated for 'chain 'E' and resid 937 through 940' Processing helix chain 'E' and resid 949 through 955 Processing helix chain 'E' and resid 962 through 977 removed outlier: 3.987A pdb=" N VAL E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR E 970 " --> pdb=" O GLY E 966 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 973 " --> pdb=" O VAL E 969 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 974 " --> pdb=" O TYR E 970 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 975 " --> pdb=" O VAL E 971 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS E 977 " --> pdb=" O GLY E 973 " (cutoff:3.500A) Processing helix chain 'E' and resid 979 through 987 removed outlier: 3.669A pdb=" N ILE E 984 " --> pdb=" O GLN E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 1433 through 1435 No H-bonds generated for 'chain 'E' and resid 1433 through 1435' Processing helix chain 'E' and resid 1480 through 1486 removed outlier: 4.241A pdb=" N GLN E1485 " --> pdb=" O HIS E1481 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN E1486 " --> pdb=" O LEU E1482 " (cutoff:3.500A) Processing helix chain 'E' and resid 1489 through 1493 removed outlier: 3.739A pdb=" N MET E1493 " --> pdb=" O LEU E1489 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1489 through 1493' Processing helix chain 'E' and resid 1523 through 1528 removed outlier: 3.515A pdb=" N ILE E1526 " --> pdb=" O CYS E1523 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU E1527 " --> pdb=" O VAL E1524 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE E1528 " --> pdb=" O CYS E1525 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1523 through 1528' Processing helix chain 'E' and resid 1610 through 1624 removed outlier: 3.950A pdb=" N LYS E1614 " --> pdb=" O ILE E1610 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E1615 " --> pdb=" O LEU E1611 " (cutoff:3.500A) Processing helix chain 'E' and resid 1629 through 1642 removed outlier: 4.105A pdb=" N ILE E1639 " --> pdb=" O GLY E1635 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E1640 " --> pdb=" O LEU E1636 " (cutoff:3.500A) Processing helix chain 'E' and resid 1650 through 1662 removed outlier: 3.716A pdb=" N HIS E1662 " --> pdb=" O HIS E1658 " (cutoff:3.500A) Processing helix chain 'E' and resid 1667 through 1672 Processing helix chain 'E' and resid 1683 through 1693 Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.622A pdb=" N ALA G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 30 No H-bonds generated for 'chain 'G' and resid 27 through 30' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.959A pdb=" N GLU G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN G 98 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 123 removed outlier: 3.856A pdb=" N LEU G 123 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 47 removed outlier: 3.812A pdb=" N ARG I 29 " --> pdb=" O ARG I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.647A pdb=" N ILE I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP I 72 " --> pdb=" O GLU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 95 Processing helix chain 'I' and resid 118 through 120 No H-bonds generated for 'chain 'I' and resid 118 through 120' Processing helix chain 'I' and resid 128 through 144 Processing helix chain 'I' and resid 167 through 177 Processing helix chain 'I' and resid 183 through 196 removed outlier: 3.584A pdb=" N ARG I 192 " --> pdb=" O GLN I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 229 No H-bonds generated for 'chain 'I' and resid 227 through 229' Processing helix chain 'I' and resid 316 through 320 Processing helix chain 'I' and resid 360 through 363 No H-bonds generated for 'chain 'I' and resid 360 through 363' Processing helix chain 'I' and resid 385 through 394 Processing sheet with id= A, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= B, first strand: chain 'A' and resid 2184 through 2188 Processing sheet with id= C, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id= D, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.921A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 315 through 321 removed outlier: 7.104A pdb=" N ALA C 18 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU C 318 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA C 16 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C 320 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE C 14 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 47 through 50 removed outlier: 4.116A pdb=" N ALA C 47 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 60 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 124 through 126 removed outlier: 4.108A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 90 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 162 through 166 removed outlier: 4.850A pdb=" N ALA C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 147 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 173 through 178 removed outlier: 7.117A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS C 194 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 216 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.606A pdb=" N LYS C 245 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 306 through 308 removed outlier: 3.543A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 289 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 990 through 992 Processing sheet with id= M, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= N, first strand: chain 'I' and resid 98 through 100 Processing sheet with id= O, first strand: chain 'I' and resid 154 through 156 Processing sheet with id= P, first strand: chain 'I' and resid 199 through 201 Processing sheet with id= Q, first strand: chain 'I' and resid 329 through 333 Processing sheet with id= R, first strand: chain 'I' and resid 342 through 344 1322 hydrogen bonds defined for protein. 3753 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: 17.03 Time building geometry restraints manager: 12.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10446 1.34 - 1.46: 6734 1.46 - 1.58: 14171 1.58 - 1.70: 6 1.70 - 1.82: 292 Bond restraints: 31649 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.588 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.596 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O16 IHP A2601 " pdb=" P6 IHP A2601 " ideal model delta sigma weight residual 1.672 1.611 0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.443 -0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 31644 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.60: 847 106.60 - 113.46: 17803 113.46 - 120.32: 11703 120.32 - 127.17: 12195 127.17 - 134.03: 383 Bond angle restraints: 42931 Sorted by residual: angle pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " ideal model delta sigma weight residual 112.00 121.28 -9.28 2.20e+00 2.07e-01 1.78e+01 angle pdb=" C GLN C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " pdb=" CZ ARG I 218 " ideal model delta sigma weight residual 124.40 128.12 -3.72 1.40e+00 5.10e-01 7.07e+00 angle pdb=" CA LEU A 811 " pdb=" CB LEU A 811 " pdb=" CG LEU A 811 " ideal model delta sigma weight residual 116.30 125.51 -9.21 3.50e+00 8.16e-02 6.93e+00 angle pdb=" C GLU E 834 " pdb=" N TYR E 835 " pdb=" CA TYR E 835 " ideal model delta sigma weight residual 122.79 118.56 4.23 1.63e+00 3.76e-01 6.72e+00 ... (remaining 42926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17295 17.92 - 35.85: 1513 35.85 - 53.77: 288 53.77 - 71.69: 46 71.69 - 89.62: 27 Dihedral angle restraints: 19169 sinusoidal: 7345 harmonic: 11824 Sorted by residual: dihedral pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " pdb=" CZ ARG I 218 " ideal model delta sinusoidal sigma weight residual -90.00 -23.20 -66.80 2 1.50e+01 4.44e-03 1.80e+01 dihedral pdb=" CA TRP E 557 " pdb=" C TRP E 557 " pdb=" N PRO E 558 " pdb=" CA PRO E 558 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR E 835 " pdb=" C TYR E 835 " pdb=" N ASN E 836 " pdb=" CA ASN E 836 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 19166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4286 0.058 - 0.116: 631 0.116 - 0.174: 30 0.174 - 0.233: 3 0.233 - 0.291: 3 Chirality restraints: 4953 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.61 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.59 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE A1048 " pdb=" CA ILE A1048 " pdb=" CG1 ILE A1048 " pdb=" CG2 ILE A1048 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4950 not shown) Planarity restraints: 5513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 51 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO C 52 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 52 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 52 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1689 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A1690 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1690 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1690 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1075 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO A1076 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1076 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1076 " -0.028 5.00e-02 4.00e+02 ... (remaining 5510 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6812 2.78 - 3.31: 30535 3.31 - 3.84: 47813 3.84 - 4.37: 57785 4.37 - 4.90: 97603 Nonbonded interactions: 240548 Sorted by model distance: nonbonded pdb=" OD2 ASP C 106 " pdb=" OG1 THR C 108 " model vdw 2.250 2.440 nonbonded pdb=" O GLN I 152 " pdb=" OG1 THR I 164 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR E1522 " pdb=" O GLN E1532 " model vdw 2.264 2.440 nonbonded pdb=" NE2 GLN C 122 " pdb=" O ARG G 111 " model vdw 2.269 2.520 nonbonded pdb=" OG1 THR C 51 " pdb=" O MET C 56 " model vdw 2.299 2.440 ... (remaining 240543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.030 Extract box with map and model: 23.850 Check model and map are aligned: 0.460 Set scattering table: 0.300 Process input model: 87.850 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.003 0.087 31649 Z= 0.211 Angle : 0.549 9.303 42931 Z= 0.282 Chirality : 0.041 0.291 4953 Planarity : 0.003 0.053 5513 Dihedral : 14.276 89.616 11455 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.33 % Allowed : 1.77 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3977 helix: 0.07 (0.11), residues: 2373 sheet: -0.56 (0.36), residues: 196 loop : -1.08 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 27 HIS 0.006 0.001 HIS I 105 PHE 0.017 0.001 PHE I 217 TYR 0.027 0.001 TYR E 835 ARG 0.008 0.001 ARG A1514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 769 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9431 (t) cc_final: 0.9155 (t) REVERT: A 630 LEU cc_start: 0.9116 (mt) cc_final: 0.8896 (tp) REVERT: A 700 LEU cc_start: 0.7325 (mp) cc_final: 0.6968 (mp) REVERT: A 701 ASN cc_start: 0.7751 (m-40) cc_final: 0.7505 (p0) REVERT: A 756 MET cc_start: 0.9078 (mtp) cc_final: 0.8747 (mmm) REVERT: A 768 ILE cc_start: 0.8018 (mm) cc_final: 0.7739 (tp) REVERT: A 772 MET cc_start: 0.8867 (mmp) cc_final: 0.8127 (mmt) REVERT: A 813 MET cc_start: 0.8302 (ttm) cc_final: 0.8086 (ttp) REVERT: A 1031 MET cc_start: 0.9153 (tpt) cc_final: 0.8920 (tpp) REVERT: A 1083 MET cc_start: 0.7527 (ppp) cc_final: 0.7286 (ppp) REVERT: A 1108 ASP cc_start: 0.8085 (m-30) cc_final: 0.7668 (p0) REVERT: A 1153 SER cc_start: 0.9080 (p) cc_final: 0.8763 (t) REVERT: A 1154 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8000 (ttt180) REVERT: A 1228 ASP cc_start: 0.8384 (t70) cc_final: 0.8095 (t0) REVERT: A 1287 LEU cc_start: 0.8866 (tp) cc_final: 0.8166 (tp) REVERT: A 1311 ASN cc_start: 0.8663 (m-40) cc_final: 0.8460 (m-40) REVERT: A 1355 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8619 (tp40) REVERT: A 1359 ASN cc_start: 0.8731 (m-40) cc_final: 0.8487 (m110) REVERT: A 1477 MET cc_start: 0.8993 (ppp) cc_final: 0.8488 (ppp) REVERT: A 1527 ASP cc_start: 0.8287 (t0) cc_final: 0.8066 (t0) REVERT: A 1530 GLU cc_start: 0.8271 (tp30) cc_final: 0.7642 (tm-30) REVERT: A 1542 ASP cc_start: 0.8528 (m-30) cc_final: 0.8256 (t0) REVERT: A 1559 LEU cc_start: 0.8791 (tp) cc_final: 0.8419 (tp) REVERT: A 1632 ASP cc_start: 0.8380 (m-30) cc_final: 0.8164 (m-30) REVERT: A 1650 MET cc_start: 0.8141 (mpp) cc_final: 0.7843 (mpp) REVERT: A 1665 ARG cc_start: 0.8279 (mpp-170) cc_final: 0.7743 (ptp90) REVERT: A 1967 TYR cc_start: 0.9068 (m-80) cc_final: 0.8776 (m-10) REVERT: A 2003 ASN cc_start: 0.8800 (t0) cc_final: 0.8470 (t0) REVERT: A 2058 MET cc_start: 0.8824 (mtt) cc_final: 0.8618 (mtt) REVERT: A 2298 ASP cc_start: 0.8940 (m-30) cc_final: 0.8066 (m-30) REVERT: A 2324 LEU cc_start: 0.9560 (tp) cc_final: 0.9358 (tp) REVERT: A 2424 ASP cc_start: 0.8928 (t0) cc_final: 0.8625 (t0) REVERT: A 2521 VAL cc_start: 0.9629 (t) cc_final: 0.8573 (t) REVERT: C 118 ASN cc_start: 0.8895 (t0) cc_final: 0.8119 (t0) REVERT: C 135 CYS cc_start: 0.7900 (t) cc_final: 0.7491 (t) REVERT: C 147 ASP cc_start: 0.8587 (p0) cc_final: 0.8093 (p0) REVERT: C 166 ILE cc_start: 0.7865 (tt) cc_final: 0.7350 (mp) REVERT: C 185 MET cc_start: 0.7222 (tmm) cc_final: 0.6557 (tmm) REVERT: C 195 TYR cc_start: 0.7237 (m-10) cc_final: 0.6797 (m-10) REVERT: C 247 TRP cc_start: 0.8488 (m100) cc_final: 0.8130 (m100) REVERT: C 255 MET cc_start: 0.8104 (tpt) cc_final: 0.7791 (mmt) REVERT: C 273 MET cc_start: 0.8138 (ttt) cc_final: 0.7843 (ttm) REVERT: C 307 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7064 (tm-30) REVERT: E 54 MET cc_start: 0.8939 (mmp) cc_final: 0.8733 (mmp) REVERT: E 81 TYR cc_start: 0.8261 (m-80) cc_final: 0.7789 (m-80) REVERT: E 124 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8106 (mmmm) REVERT: E 247 ASP cc_start: 0.8048 (m-30) cc_final: 0.7797 (t0) REVERT: E 249 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7893 (mm-30) REVERT: E 251 GLU cc_start: 0.8768 (mp0) cc_final: 0.8348 (mt-10) REVERT: E 372 GLU cc_start: 0.8357 (tt0) cc_final: 0.8046 (pt0) REVERT: E 475 CYS cc_start: 0.8388 (m) cc_final: 0.8012 (m) REVERT: E 523 ASP cc_start: 0.5638 (m-30) cc_final: 0.5412 (m-30) REVERT: E 545 GLU cc_start: 0.6209 (tp30) cc_final: 0.5787 (tp30) REVERT: E 564 ASN cc_start: 0.8058 (m110) cc_final: 0.7735 (t0) REVERT: E 565 TYR cc_start: 0.4667 (m-80) cc_final: 0.3983 (m-10) REVERT: E 577 LEU cc_start: 0.9259 (tp) cc_final: 0.8934 (tt) REVERT: E 684 CYS cc_start: 0.8833 (t) cc_final: 0.8573 (t) REVERT: E 696 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7222 (p90) REVERT: E 737 ARG cc_start: 0.8391 (ttm170) cc_final: 0.7984 (ptp-110) REVERT: E 775 ASP cc_start: 0.8744 (t70) cc_final: 0.8543 (t0) REVERT: E 779 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7438 (tm-30) REVERT: E 1424 TYR cc_start: 0.8818 (m-10) cc_final: 0.8595 (m-10) REVERT: E 1514 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8005 (tm-30) REVERT: E 1642 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8229 (tptt) REVERT: G 26 MET cc_start: 0.7837 (mmt) cc_final: 0.6967 (mmm) REVERT: G 27 CYS cc_start: 0.9197 (m) cc_final: 0.8551 (m) REVERT: I 23 GLN cc_start: 0.3418 (OUTLIER) cc_final: 0.3156 (pp30) REVERT: I 134 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9029 (ptt) REVERT: I 149 THR cc_start: 0.3566 (OUTLIER) cc_final: 0.3134 (p) REVERT: I 164 THR cc_start: 0.1175 (OUTLIER) cc_final: 0.0520 (p) REVERT: I 171 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6946 (mt) REVERT: I 212 ASN cc_start: 0.9043 (p0) cc_final: 0.8657 (t0) REVERT: I 219 MET cc_start: 0.8681 (tpp) cc_final: 0.8289 (tmm) REVERT: I 319 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8662 (tt) REVERT: I 326 TYR cc_start: 0.6928 (p90) cc_final: 0.6452 (p90) REVERT: I 376 ASN cc_start: 0.8853 (p0) cc_final: 0.8319 (m-40) REVERT: I 403 VAL cc_start: 0.7675 (m) cc_final: 0.7165 (m) outliers start: 42 outliers final: 10 residues processed: 800 average time/residue: 0.4987 time to fit residues: 621.0563 Evaluate side-chains 437 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 420 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 314 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 364 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 HIS ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1719 HIS A1758 GLN A2099 GLN C 64 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS E 683 GLN E 908 ASN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN I 390 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31649 Z= 0.216 Angle : 0.626 13.552 42931 Z= 0.316 Chirality : 0.042 0.324 4953 Planarity : 0.004 0.050 5513 Dihedral : 5.115 71.762 4408 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.22 % Allowed : 11.15 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3977 helix: 0.49 (0.11), residues: 2367 sheet: -0.43 (0.37), residues: 189 loop : -1.06 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1269 HIS 0.006 0.001 HIS C 64 PHE 0.019 0.001 PHE E 611 TYR 0.026 0.002 TYR A2542 ARG 0.008 0.001 ARG A2152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 463 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9422 (t) cc_final: 0.9107 (t) REVERT: A 620 MET cc_start: 0.8332 (tpp) cc_final: 0.8072 (mmt) REVERT: A 679 LEU cc_start: 0.9608 (mm) cc_final: 0.9396 (mm) REVERT: A 700 LEU cc_start: 0.7366 (mp) cc_final: 0.6939 (mp) REVERT: A 701 ASN cc_start: 0.7712 (m-40) cc_final: 0.7478 (p0) REVERT: A 756 MET cc_start: 0.9024 (mtp) cc_final: 0.8810 (mmm) REVERT: A 768 ILE cc_start: 0.8272 (mm) cc_final: 0.8016 (tp) REVERT: A 772 MET cc_start: 0.8675 (mmp) cc_final: 0.8468 (mmt) REVERT: A 816 TRP cc_start: 0.8276 (m100) cc_final: 0.7615 (m100) REVERT: A 1083 MET cc_start: 0.7433 (ppp) cc_final: 0.7165 (ppp) REVERT: A 1108 ASP cc_start: 0.8101 (m-30) cc_final: 0.7829 (p0) REVERT: A 1153 SER cc_start: 0.9246 (p) cc_final: 0.8932 (t) REVERT: A 1154 ARG cc_start: 0.8599 (tpp80) cc_final: 0.8281 (ttt180) REVERT: A 1228 ASP cc_start: 0.8122 (t70) cc_final: 0.7834 (t0) REVERT: A 1359 ASN cc_start: 0.8768 (m-40) cc_final: 0.8351 (m110) REVERT: A 1477 MET cc_start: 0.8343 (ppp) cc_final: 0.8071 (ppp) REVERT: A 1515 MET cc_start: 0.7900 (mtm) cc_final: 0.7646 (mtm) REVERT: A 1530 GLU cc_start: 0.8216 (tp30) cc_final: 0.7632 (tm-30) REVERT: A 1542 ASP cc_start: 0.8536 (m-30) cc_final: 0.8254 (t0) REVERT: A 1555 ASP cc_start: 0.8785 (m-30) cc_final: 0.8571 (t0) REVERT: A 1638 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8408 (tpp) REVERT: A 1650 MET cc_start: 0.8121 (mpp) cc_final: 0.7811 (mpp) REVERT: A 1701 MET cc_start: 0.8996 (mtm) cc_final: 0.8717 (mtm) REVERT: A 1717 MET cc_start: 0.9414 (tpp) cc_final: 0.8949 (tpp) REVERT: A 1747 MET cc_start: 0.9037 (mmp) cc_final: 0.8808 (mmm) REVERT: A 1928 LYS cc_start: 0.9238 (ptpp) cc_final: 0.9031 (pttm) REVERT: A 2298 ASP cc_start: 0.8656 (m-30) cc_final: 0.7736 (m-30) REVERT: A 2424 ASP cc_start: 0.8917 (t0) cc_final: 0.8656 (t0) REVERT: C 68 TYR cc_start: 0.7366 (m-80) cc_final: 0.7119 (m-80) REVERT: C 135 CYS cc_start: 0.7909 (t) cc_final: 0.7435 (t) REVERT: C 147 ASP cc_start: 0.8642 (p0) cc_final: 0.8224 (p0) REVERT: C 184 TYR cc_start: 0.8224 (m-80) cc_final: 0.7966 (m-80) REVERT: C 185 MET cc_start: 0.7193 (tmm) cc_final: 0.6783 (tmm) REVERT: C 195 TYR cc_start: 0.7330 (m-80) cc_final: 0.6965 (m-10) REVERT: C 255 MET cc_start: 0.8219 (tpt) cc_final: 0.7925 (mmt) REVERT: C 273 MET cc_start: 0.8173 (ttt) cc_final: 0.7851 (ttm) REVERT: E 124 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8087 (mmmm) REVERT: E 247 ASP cc_start: 0.7987 (m-30) cc_final: 0.7614 (t0) REVERT: E 251 GLU cc_start: 0.8744 (mp0) cc_final: 0.8334 (mt-10) REVERT: E 372 GLU cc_start: 0.8342 (tt0) cc_final: 0.7969 (pt0) REVERT: E 475 CYS cc_start: 0.8663 (m) cc_final: 0.8204 (m) REVERT: E 565 TYR cc_start: 0.4434 (m-80) cc_final: 0.3988 (m-10) REVERT: E 696 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.7047 (p90) REVERT: E 779 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7651 (tm-30) REVERT: E 1514 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7920 (tm-30) REVERT: E 1642 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8343 (tptt) REVERT: G 27 CYS cc_start: 0.9142 (m) cc_final: 0.8857 (m) REVERT: G 89 ARG cc_start: 0.9185 (mtp180) cc_final: 0.8365 (mtp180) REVERT: I 148 ASN cc_start: 0.7392 (t0) cc_final: 0.6724 (t0) REVERT: I 149 THR cc_start: 0.3644 (OUTLIER) cc_final: 0.1586 (p) REVERT: I 164 THR cc_start: 0.0790 (OUTLIER) cc_final: 0.0372 (p) REVERT: I 212 ASN cc_start: 0.9045 (p0) cc_final: 0.8798 (t0) REVERT: I 219 MET cc_start: 0.8606 (tpp) cc_final: 0.8208 (tmm) REVERT: I 228 MET cc_start: 0.4096 (tpt) cc_final: 0.3130 (mmt) REVERT: I 319 LEU cc_start: 0.8787 (tp) cc_final: 0.8581 (tp) REVERT: I 376 ASN cc_start: 0.8869 (p0) cc_final: 0.8322 (m-40) outliers start: 70 outliers final: 37 residues processed: 515 average time/residue: 0.4162 time to fit residues: 349.5922 Evaluate side-chains 407 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 366 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1505 ASN Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1638 MET Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 390 ASN Chi-restraints excluded: chain I residue 401 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 202 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 364 optimal weight: 0.0670 chunk 394 optimal weight: 0.9990 chunk 324 optimal weight: 0.3980 chunk 361 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN A1806 HIS A2099 GLN A2200 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 ASN ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31649 Z= 0.165 Angle : 0.546 11.472 42931 Z= 0.275 Chirality : 0.040 0.398 4953 Planarity : 0.004 0.047 5513 Dihedral : 4.607 59.934 4397 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.38 % Allowed : 13.12 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 3977 helix: 0.84 (0.11), residues: 2350 sheet: -0.31 (0.38), residues: 187 loop : -1.06 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1269 HIS 0.006 0.001 HIS A1084 PHE 0.022 0.001 PHE E 611 TYR 0.028 0.001 TYR A2542 ARG 0.008 0.000 ARG I 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 397 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9388 (t) cc_final: 0.9037 (t) REVERT: A 620 MET cc_start: 0.8319 (tpp) cc_final: 0.7957 (mmt) REVERT: A 700 LEU cc_start: 0.7258 (mp) cc_final: 0.6852 (mp) REVERT: A 701 ASN cc_start: 0.7706 (m-40) cc_final: 0.7457 (p0) REVERT: A 756 MET cc_start: 0.8981 (mtp) cc_final: 0.8778 (mmm) REVERT: A 768 ILE cc_start: 0.8358 (mm) cc_final: 0.8028 (tp) REVERT: A 816 TRP cc_start: 0.8188 (m100) cc_final: 0.7609 (m100) REVERT: A 853 TYR cc_start: 0.8219 (t80) cc_final: 0.7997 (t80) REVERT: A 1083 MET cc_start: 0.7571 (ppp) cc_final: 0.7275 (ppp) REVERT: A 1108 ASP cc_start: 0.8170 (m-30) cc_final: 0.7915 (p0) REVERT: A 1153 SER cc_start: 0.9218 (p) cc_final: 0.8874 (t) REVERT: A 1154 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8207 (ttt180) REVERT: A 1155 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7676 (mt) REVERT: A 1477 MET cc_start: 0.8325 (ppp) cc_final: 0.7879 (ppp) REVERT: A 1521 TRP cc_start: 0.9044 (t60) cc_final: 0.8781 (t60) REVERT: A 1555 ASP cc_start: 0.8779 (m-30) cc_final: 0.8575 (t0) REVERT: A 1638 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8490 (tpp) REVERT: A 1650 MET cc_start: 0.8035 (mpp) cc_final: 0.7742 (mpp) REVERT: A 1717 MET cc_start: 0.9355 (tpp) cc_final: 0.9132 (tpp) REVERT: A 1928 LYS cc_start: 0.9227 (ptpp) cc_final: 0.8974 (pttm) REVERT: A 2298 ASP cc_start: 0.8667 (m-30) cc_final: 0.7904 (m-30) REVERT: A 2424 ASP cc_start: 0.8916 (t0) cc_final: 0.8693 (t0) REVERT: C 63 GLN cc_start: 0.7418 (mt0) cc_final: 0.6932 (mt0) REVERT: C 86 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6820 (mmmt) REVERT: C 135 CYS cc_start: 0.7878 (t) cc_final: 0.7454 (t) REVERT: C 147 ASP cc_start: 0.8658 (p0) cc_final: 0.8197 (p0) REVERT: C 184 TYR cc_start: 0.8169 (m-80) cc_final: 0.7920 (m-80) REVERT: C 185 MET cc_start: 0.7200 (tmm) cc_final: 0.6809 (tmm) REVERT: C 195 TYR cc_start: 0.7333 (m-80) cc_final: 0.6956 (m-10) REVERT: C 258 LEU cc_start: 0.7843 (mp) cc_final: 0.7336 (tt) REVERT: C 273 MET cc_start: 0.8193 (ttt) cc_final: 0.7834 (ttm) REVERT: E 81 TYR cc_start: 0.8208 (m-80) cc_final: 0.7981 (m-80) REVERT: E 124 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8095 (mmmm) REVERT: E 224 ASN cc_start: 0.8820 (t0) cc_final: 0.8532 (m-40) REVERT: E 247 ASP cc_start: 0.7909 (m-30) cc_final: 0.7504 (t0) REVERT: E 248 VAL cc_start: 0.9268 (m) cc_final: 0.8983 (t) REVERT: E 251 GLU cc_start: 0.8789 (mp0) cc_final: 0.7987 (mp0) REVERT: E 475 CYS cc_start: 0.8654 (m) cc_final: 0.8241 (m) REVERT: E 592 ASP cc_start: 0.8431 (t0) cc_final: 0.8188 (t0) REVERT: E 675 MET cc_start: 0.8469 (mmm) cc_final: 0.8042 (tpp) REVERT: E 1487 MET cc_start: 0.8580 (pmm) cc_final: 0.8292 (pmm) REVERT: E 1514 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8015 (tm-30) REVERT: E 1642 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8345 (tptt) REVERT: G 27 CYS cc_start: 0.9188 (m) cc_final: 0.8668 (m) REVERT: G 89 ARG cc_start: 0.9044 (mtp180) cc_final: 0.8647 (mtp180) REVERT: G 91 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7996 (tm-30) REVERT: I 134 MET cc_start: 0.9307 (ptt) cc_final: 0.9096 (mmm) REVERT: I 164 THR cc_start: 0.0989 (OUTLIER) cc_final: 0.0720 (p) REVERT: I 166 MET cc_start: 0.9015 (mmt) cc_final: 0.8585 (mmm) REVERT: I 190 CYS cc_start: 0.9665 (m) cc_final: 0.9398 (p) REVERT: I 212 ASN cc_start: 0.9008 (p0) cc_final: 0.8693 (t0) REVERT: I 219 MET cc_start: 0.8595 (tpp) cc_final: 0.8363 (tmm) REVERT: I 228 MET cc_start: 0.4037 (tpt) cc_final: 0.3096 (mmt) REVERT: I 376 ASN cc_start: 0.8896 (p0) cc_final: 0.8344 (m-40) outliers start: 75 outliers final: 47 residues processed: 450 average time/residue: 0.4190 time to fit residues: 310.9167 Evaluate side-chains 399 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 349 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1227 GLU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1638 MET Chi-restraints excluded: chain A residue 1660 CYS Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1492 ILE Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 393 LEU Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 360 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 387 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 346 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1084 HIS A2099 GLN C 64 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN E 564 ASN E 683 GLN E 758 GLN E 827 GLN I 24 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31649 Z= 0.198 Angle : 0.537 15.371 42931 Z= 0.269 Chirality : 0.040 0.368 4953 Planarity : 0.003 0.043 5513 Dihedral : 4.338 58.107 4389 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.69 % Allowed : 14.45 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.14), residues: 3977 helix: 1.04 (0.11), residues: 2360 sheet: -0.36 (0.38), residues: 189 loop : -1.05 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2429 HIS 0.018 0.001 HIS A1806 PHE 0.022 0.001 PHE E 611 TYR 0.029 0.001 TYR A2542 ARG 0.009 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 365 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9448 (t) cc_final: 0.9128 (t) REVERT: A 620 MET cc_start: 0.8276 (tpp) cc_final: 0.7913 (mmt) REVERT: A 679 LEU cc_start: 0.9618 (mm) cc_final: 0.9316 (tp) REVERT: A 772 MET cc_start: 0.8539 (mmp) cc_final: 0.8155 (mmt) REVERT: A 816 TRP cc_start: 0.8296 (m100) cc_final: 0.7639 (m100) REVERT: A 853 TYR cc_start: 0.8292 (t80) cc_final: 0.8006 (t80) REVERT: A 1083 MET cc_start: 0.7712 (ppp) cc_final: 0.7409 (ppp) REVERT: A 1108 ASP cc_start: 0.8266 (m-30) cc_final: 0.7957 (p0) REVERT: A 1153 SER cc_start: 0.9210 (p) cc_final: 0.8847 (t) REVERT: A 1154 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8213 (ttt180) REVERT: A 1155 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7787 (mt) REVERT: A 1194 MET cc_start: 0.8793 (tmm) cc_final: 0.8196 (tmm) REVERT: A 1530 GLU cc_start: 0.8190 (tp30) cc_final: 0.7593 (tm-30) REVERT: A 1555 ASP cc_start: 0.8843 (m-30) cc_final: 0.8572 (t0) REVERT: A 1578 MET cc_start: 0.8345 (mmp) cc_final: 0.7914 (mtt) REVERT: A 1650 MET cc_start: 0.8034 (mpp) cc_final: 0.7744 (mpp) REVERT: A 1717 MET cc_start: 0.9317 (tpp) cc_final: 0.9017 (tpp) REVERT: A 1928 LYS cc_start: 0.9242 (ptpp) cc_final: 0.8994 (pttm) REVERT: A 2175 MET cc_start: 0.8849 (tpp) cc_final: 0.8588 (tpt) REVERT: A 2298 ASP cc_start: 0.8744 (m-30) cc_final: 0.7960 (m-30) REVERT: A 2424 ASP cc_start: 0.8952 (t0) cc_final: 0.8708 (t0) REVERT: C 51 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 143 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6826 (mt) REVERT: C 147 ASP cc_start: 0.8656 (p0) cc_final: 0.8097 (p0) REVERT: C 184 TYR cc_start: 0.8181 (m-80) cc_final: 0.7931 (m-80) REVERT: C 185 MET cc_start: 0.7316 (tmm) cc_final: 0.6926 (tmm) REVERT: C 195 TYR cc_start: 0.7328 (m-80) cc_final: 0.6980 (m-10) REVERT: C 258 LEU cc_start: 0.7581 (mp) cc_final: 0.7226 (tt) REVERT: C 273 MET cc_start: 0.8258 (ttt) cc_final: 0.7847 (ttm) REVERT: C 307 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7155 (tm-30) REVERT: E 81 TYR cc_start: 0.8303 (m-80) cc_final: 0.8036 (m-80) REVERT: E 124 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8118 (mmmm) REVERT: E 224 ASN cc_start: 0.8846 (t0) cc_final: 0.8543 (m-40) REVERT: E 475 CYS cc_start: 0.8630 (m) cc_final: 0.8194 (m) REVERT: E 545 GLU cc_start: 0.6195 (tp30) cc_final: 0.5705 (tp30) REVERT: E 561 ASN cc_start: 0.6443 (OUTLIER) cc_final: 0.5768 (t0) REVERT: E 675 MET cc_start: 0.8553 (mmm) cc_final: 0.8044 (tpp) REVERT: E 1514 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8040 (tm-30) REVERT: E 1642 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8308 (tptt) REVERT: G 27 CYS cc_start: 0.9303 (m) cc_final: 0.8777 (m) REVERT: G 89 ARG cc_start: 0.8987 (mtp180) cc_final: 0.8741 (mtp180) REVERT: I 149 THR cc_start: 0.4131 (OUTLIER) cc_final: 0.3678 (p) REVERT: I 164 THR cc_start: 0.1277 (OUTLIER) cc_final: 0.1035 (p) REVERT: I 166 MET cc_start: 0.9070 (mmt) cc_final: 0.8679 (mmm) REVERT: I 212 ASN cc_start: 0.9019 (p0) cc_final: 0.8749 (t0) REVERT: I 228 MET cc_start: 0.4285 (tpt) cc_final: 0.3358 (mmt) REVERT: I 376 ASN cc_start: 0.8941 (p0) cc_final: 0.8355 (m-40) outliers start: 85 outliers final: 55 residues processed: 427 average time/residue: 0.4562 time to fit residues: 327.9838 Evaluate side-chains 390 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 329 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1084 HIS Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1632 ASP Chi-restraints excluded: chain A residue 1660 CYS Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2099 GLN Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2419 GLU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 744 VAL Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 393 LEU Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 322 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 330 optimal weight: 0.3980 chunk 267 optimal weight: 0.5980 chunk 0 optimal weight: 50.0000 chunk 197 optimal weight: 0.8980 chunk 347 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2099 GLN ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS G 88 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31649 Z= 0.157 Angle : 0.516 10.619 42931 Z= 0.258 Chirality : 0.039 0.254 4953 Planarity : 0.003 0.041 5513 Dihedral : 4.225 58.010 4387 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.82 % Allowed : 15.81 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3977 helix: 1.18 (0.11), residues: 2364 sheet: -0.26 (0.38), residues: 194 loop : -1.03 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A2429 HIS 0.013 0.001 HIS A1084 PHE 0.011 0.001 PHE E 79 TYR 0.029 0.001 TYR A2542 ARG 0.004 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 354 time to evaluate : 3.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9458 (t) cc_final: 0.9144 (t) REVERT: A 620 MET cc_start: 0.8241 (tpp) cc_final: 0.7843 (mmt) REVERT: A 630 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9049 (tp) REVERT: A 679 LEU cc_start: 0.9612 (mm) cc_final: 0.9327 (tp) REVERT: A 772 MET cc_start: 0.8493 (mmp) cc_final: 0.8248 (mmp) REVERT: A 816 TRP cc_start: 0.8229 (m100) cc_final: 0.7462 (m100) REVERT: A 853 TYR cc_start: 0.8191 (t80) cc_final: 0.7517 (t80) REVERT: A 1108 ASP cc_start: 0.8267 (m-30) cc_final: 0.7958 (p0) REVERT: A 1153 SER cc_start: 0.9221 (p) cc_final: 0.8855 (t) REVERT: A 1154 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8192 (ttt180) REVERT: A 1155 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7761 (mt) REVERT: A 1313 MET cc_start: 0.8656 (ppp) cc_final: 0.8264 (tmm) REVERT: A 1555 ASP cc_start: 0.8818 (m-30) cc_final: 0.8543 (t0) REVERT: A 1650 MET cc_start: 0.8002 (mpp) cc_final: 0.7739 (mpp) REVERT: A 1717 MET cc_start: 0.9297 (tpp) cc_final: 0.8987 (tpp) REVERT: A 2041 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8488 (tm-30) REVERT: A 2099 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: A 2424 ASP cc_start: 0.8914 (t0) cc_final: 0.8689 (t0) REVERT: A 2516 ASP cc_start: 0.8686 (m-30) cc_final: 0.7637 (p0) REVERT: C 68 TYR cc_start: 0.7047 (m-80) cc_final: 0.6820 (m-80) REVERT: C 86 LYS cc_start: 0.7134 (mmmt) cc_final: 0.6859 (mmmt) REVERT: C 147 ASP cc_start: 0.8644 (p0) cc_final: 0.8024 (p0) REVERT: C 184 TYR cc_start: 0.8201 (m-80) cc_final: 0.7956 (m-80) REVERT: C 185 MET cc_start: 0.7363 (tmm) cc_final: 0.6973 (tmm) REVERT: C 195 TYR cc_start: 0.7321 (m-80) cc_final: 0.6985 (m-10) REVERT: C 258 LEU cc_start: 0.7612 (mp) cc_final: 0.7235 (tt) REVERT: C 273 MET cc_start: 0.8207 (ttt) cc_final: 0.7835 (ttm) REVERT: E 81 TYR cc_start: 0.8294 (m-80) cc_final: 0.8057 (m-80) REVERT: E 124 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8055 (mmmm) REVERT: E 224 ASN cc_start: 0.8806 (t0) cc_final: 0.8563 (m-40) REVERT: E 251 GLU cc_start: 0.8583 (mp0) cc_final: 0.7813 (mp0) REVERT: E 475 CYS cc_start: 0.8705 (m) cc_final: 0.8231 (m) REVERT: E 545 GLU cc_start: 0.6212 (tp30) cc_final: 0.5724 (tp30) REVERT: E 561 ASN cc_start: 0.6478 (OUTLIER) cc_final: 0.5738 (t0) REVERT: E 675 MET cc_start: 0.8488 (mmm) cc_final: 0.8016 (tpp) REVERT: E 769 GLU cc_start: 0.7944 (tp30) cc_final: 0.7693 (tp30) REVERT: E 1514 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8030 (tm-30) REVERT: E 1607 MET cc_start: 0.5834 (mmp) cc_final: 0.5594 (mmm) REVERT: E 1642 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8313 (tptt) REVERT: G 27 CYS cc_start: 0.9262 (m) cc_final: 0.8702 (m) REVERT: G 89 ARG cc_start: 0.9009 (mtp180) cc_final: 0.8774 (mtp180) REVERT: G 91 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8251 (tm-30) REVERT: I 134 MET cc_start: 0.9571 (ptt) cc_final: 0.9217 (mmm) REVERT: I 149 THR cc_start: 0.4733 (OUTLIER) cc_final: 0.4334 (p) REVERT: I 164 THR cc_start: 0.1294 (OUTLIER) cc_final: 0.1058 (p) REVERT: I 166 MET cc_start: 0.9147 (mmt) cc_final: 0.8743 (mmm) REVERT: I 212 ASN cc_start: 0.9011 (p0) cc_final: 0.8734 (t0) REVERT: I 228 MET cc_start: 0.4315 (tpt) cc_final: 0.3395 (mmt) REVERT: I 376 ASN cc_start: 0.9001 (p0) cc_final: 0.8349 (m-40) outliers start: 89 outliers final: 53 residues processed: 417 average time/residue: 0.3994 time to fit residues: 277.9400 Evaluate side-chains 390 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 331 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1660 CYS Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2099 GLN Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2419 GLU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 130 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 76 optimal weight: 0.0570 chunk 227 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 chunk 387 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 203 optimal weight: 0.1980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2099 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31649 Z= 0.156 Angle : 0.523 13.888 42931 Z= 0.259 Chirality : 0.039 0.251 4953 Planarity : 0.003 0.039 5513 Dihedral : 4.183 57.313 4387 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.50 % Allowed : 16.92 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3977 helix: 1.30 (0.11), residues: 2364 sheet: -0.24 (0.38), residues: 194 loop : -1.00 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2429 HIS 0.006 0.001 HIS C 64 PHE 0.011 0.001 PHE E 79 TYR 0.030 0.001 TYR A2542 ARG 0.019 0.000 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 349 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9420 (t) cc_final: 0.9111 (t) REVERT: A 620 MET cc_start: 0.8182 (tpp) cc_final: 0.7810 (mmt) REVERT: A 630 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9040 (tp) REVERT: A 679 LEU cc_start: 0.9609 (mm) cc_final: 0.9315 (tp) REVERT: A 768 ILE cc_start: 0.8042 (tp) cc_final: 0.7790 (tp) REVERT: A 772 MET cc_start: 0.8483 (mmp) cc_final: 0.8222 (mmp) REVERT: A 853 TYR cc_start: 0.8148 (t80) cc_final: 0.7431 (t80) REVERT: A 1108 ASP cc_start: 0.8256 (m-30) cc_final: 0.7960 (p0) REVERT: A 1153 SER cc_start: 0.9229 (p) cc_final: 0.8855 (t) REVERT: A 1154 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8236 (ttt180) REVERT: A 1155 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7754 (mt) REVERT: A 1171 SER cc_start: 0.8194 (m) cc_final: 0.7898 (p) REVERT: A 1313 MET cc_start: 0.8646 (ppp) cc_final: 0.8230 (tmm) REVERT: A 1555 ASP cc_start: 0.8825 (m-30) cc_final: 0.8558 (t0) REVERT: A 1578 MET cc_start: 0.8430 (mmp) cc_final: 0.7967 (mtt) REVERT: A 1638 MET cc_start: 0.8779 (tpp) cc_final: 0.8251 (tpp) REVERT: A 1650 MET cc_start: 0.7965 (mpp) cc_final: 0.7716 (mpp) REVERT: A 2041 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8431 (tm-30) REVERT: A 2099 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: A 2424 ASP cc_start: 0.8933 (t0) cc_final: 0.8708 (t0) REVERT: A 2516 ASP cc_start: 0.8684 (m-30) cc_final: 0.7615 (p0) REVERT: C 142 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6775 (mp0) REVERT: C 143 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6617 (mt) REVERT: C 147 ASP cc_start: 0.8632 (p0) cc_final: 0.8037 (p0) REVERT: C 184 TYR cc_start: 0.8228 (m-80) cc_final: 0.7961 (m-80) REVERT: C 185 MET cc_start: 0.7363 (tmm) cc_final: 0.6992 (tmm) REVERT: C 195 TYR cc_start: 0.7300 (m-80) cc_final: 0.6854 (m-10) REVERT: C 258 LEU cc_start: 0.7708 (mp) cc_final: 0.7306 (tt) REVERT: C 273 MET cc_start: 0.8224 (ttt) cc_final: 0.7824 (ttm) REVERT: E 81 TYR cc_start: 0.8292 (m-80) cc_final: 0.8059 (m-80) REVERT: E 124 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8020 (mmmm) REVERT: E 183 MET cc_start: 0.8742 (mtp) cc_final: 0.8496 (ttm) REVERT: E 224 ASN cc_start: 0.8787 (t0) cc_final: 0.8576 (m-40) REVERT: E 475 CYS cc_start: 0.8672 (m) cc_final: 0.8203 (m) REVERT: E 504 THR cc_start: 0.8872 (m) cc_final: 0.8650 (p) REVERT: E 545 GLU cc_start: 0.6239 (tp30) cc_final: 0.5740 (tp30) REVERT: E 561 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.5790 (t0) REVERT: E 592 ASP cc_start: 0.8453 (t0) cc_final: 0.8197 (t0) REVERT: E 675 MET cc_start: 0.8503 (mmm) cc_final: 0.8065 (tpp) REVERT: E 1642 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8301 (tptt) REVERT: G 27 CYS cc_start: 0.9205 (m) cc_final: 0.8693 (m) REVERT: G 88 GLN cc_start: 0.8991 (mm110) cc_final: 0.8370 (mp10) REVERT: G 91 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8161 (tm-30) REVERT: I 134 MET cc_start: 0.9616 (ptt) cc_final: 0.9268 (mmm) REVERT: I 149 THR cc_start: 0.4816 (OUTLIER) cc_final: 0.4429 (p) REVERT: I 164 THR cc_start: 0.0991 (OUTLIER) cc_final: 0.0758 (p) REVERT: I 212 ASN cc_start: 0.9034 (p0) cc_final: 0.8711 (t0) REVERT: I 228 MET cc_start: 0.4319 (tpt) cc_final: 0.3419 (mmt) REVERT: I 376 ASN cc_start: 0.9082 (p0) cc_final: 0.8364 (m-40) outliers start: 79 outliers final: 54 residues processed: 405 average time/residue: 0.4114 time to fit residues: 275.7420 Evaluate side-chains 392 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 331 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1660 CYS Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2099 GLN Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain A residue 2419 GLU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 374 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 283 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 326 optimal weight: 0.0470 chunk 216 optimal weight: 0.9990 chunk 386 optimal weight: 0.9980 chunk 241 optimal weight: 0.4980 chunk 235 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1604 GLN A1806 HIS A2099 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31649 Z= 0.155 Angle : 0.520 10.833 42931 Z= 0.258 Chirality : 0.039 0.224 4953 Planarity : 0.003 0.039 5513 Dihedral : 4.160 56.644 4387 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.44 % Allowed : 17.27 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3977 helix: 1.39 (0.11), residues: 2367 sheet: -0.05 (0.40), residues: 182 loop : -0.99 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2429 HIS 0.027 0.001 HIS C 64 PHE 0.011 0.001 PHE A 306 TYR 0.030 0.001 TYR A2542 ARG 0.010 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 352 time to evaluate : 3.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9429 (t) cc_final: 0.9125 (t) REVERT: A 620 MET cc_start: 0.8200 (tpp) cc_final: 0.7829 (mmt) REVERT: A 630 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9043 (tp) REVERT: A 679 LEU cc_start: 0.9606 (mm) cc_final: 0.9323 (tp) REVERT: A 768 ILE cc_start: 0.8188 (tp) cc_final: 0.7923 (tp) REVERT: A 772 MET cc_start: 0.8483 (mmp) cc_final: 0.8200 (mmp) REVERT: A 816 TRP cc_start: 0.8163 (m100) cc_final: 0.7911 (m100) REVERT: A 853 TYR cc_start: 0.8133 (t80) cc_final: 0.7491 (t80) REVERT: A 1018 MET cc_start: 0.9175 (mmm) cc_final: 0.8877 (mpp) REVERT: A 1153 SER cc_start: 0.9227 (p) cc_final: 0.8849 (t) REVERT: A 1154 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8253 (ttt180) REVERT: A 1171 SER cc_start: 0.8195 (m) cc_final: 0.7914 (p) REVERT: A 1194 MET cc_start: 0.8751 (tmm) cc_final: 0.8231 (tmm) REVERT: A 1231 ILE cc_start: 0.9201 (tp) cc_final: 0.8810 (tp) REVERT: A 1313 MET cc_start: 0.8675 (ppp) cc_final: 0.8251 (tmm) REVERT: A 1467 MET cc_start: 0.8198 (mmm) cc_final: 0.7898 (mmm) REVERT: A 1555 ASP cc_start: 0.8831 (m-30) cc_final: 0.8561 (t0) REVERT: A 1578 MET cc_start: 0.8470 (mmp) cc_final: 0.7858 (mtt) REVERT: A 1638 MET cc_start: 0.8820 (tpp) cc_final: 0.8300 (tpp) REVERT: A 1650 MET cc_start: 0.7963 (mpp) cc_final: 0.7738 (mpp) REVERT: A 1796 MET cc_start: 0.8869 (tpp) cc_final: 0.8466 (tpt) REVERT: A 2041 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8463 (tm-30) REVERT: A 2099 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: A 2132 MET cc_start: 0.8281 (ptt) cc_final: 0.8059 (ptt) REVERT: A 2424 ASP cc_start: 0.8917 (t0) cc_final: 0.8695 (t0) REVERT: A 2516 ASP cc_start: 0.8678 (m-30) cc_final: 0.7578 (p0) REVERT: C 86 LYS cc_start: 0.6900 (mmmt) cc_final: 0.6516 (mmmt) REVERT: C 118 ASN cc_start: 0.8730 (t0) cc_final: 0.8114 (t0) REVERT: C 142 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6651 (mp0) REVERT: C 143 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6596 (mp) REVERT: C 147 ASP cc_start: 0.8616 (p0) cc_final: 0.8220 (p0) REVERT: C 184 TYR cc_start: 0.8242 (m-80) cc_final: 0.7980 (m-80) REVERT: C 185 MET cc_start: 0.7362 (tmm) cc_final: 0.7007 (tmm) REVERT: C 195 TYR cc_start: 0.7247 (m-80) cc_final: 0.6748 (m-10) REVERT: C 258 LEU cc_start: 0.7688 (mp) cc_final: 0.7361 (tt) REVERT: C 273 MET cc_start: 0.8220 (ttt) cc_final: 0.7813 (ttm) REVERT: E 124 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8042 (mmmm) REVERT: E 142 GLU cc_start: 0.7639 (tp30) cc_final: 0.7338 (tp30) REVERT: E 183 MET cc_start: 0.8746 (mtp) cc_final: 0.8497 (ttm) REVERT: E 224 ASN cc_start: 0.8790 (t0) cc_final: 0.8570 (m-40) REVERT: E 351 LEU cc_start: 0.9088 (tp) cc_final: 0.8796 (mm) REVERT: E 475 CYS cc_start: 0.8685 (m) cc_final: 0.8217 (m) REVERT: E 504 THR cc_start: 0.8865 (m) cc_final: 0.8651 (p) REVERT: E 545 GLU cc_start: 0.6276 (tp30) cc_final: 0.5769 (tp30) REVERT: E 561 ASN cc_start: 0.6552 (OUTLIER) cc_final: 0.5871 (t0) REVERT: E 592 ASP cc_start: 0.8453 (t0) cc_final: 0.8194 (t0) REVERT: E 675 MET cc_start: 0.8488 (mmm) cc_final: 0.8078 (tpp) REVERT: E 1607 MET cc_start: 0.5916 (mmp) cc_final: 0.5655 (mmm) REVERT: E 1642 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8286 (tptt) REVERT: G 27 CYS cc_start: 0.9134 (m) cc_final: 0.8646 (m) REVERT: G 88 GLN cc_start: 0.8841 (mm110) cc_final: 0.8547 (mp10) REVERT: I 164 THR cc_start: 0.0948 (OUTLIER) cc_final: 0.0704 (p) REVERT: I 212 ASN cc_start: 0.9049 (p0) cc_final: 0.8723 (t0) REVERT: I 228 MET cc_start: 0.4298 (tpt) cc_final: 0.3399 (mmt) REVERT: I 326 TYR cc_start: 0.6991 (p90) cc_final: 0.6774 (p90) REVERT: I 376 ASN cc_start: 0.9088 (p0) cc_final: 0.8367 (m-40) outliers start: 77 outliers final: 54 residues processed: 409 average time/residue: 0.3917 time to fit residues: 270.0877 Evaluate side-chains 397 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1660 CYS Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2099 GLN Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 382 HIS Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 239 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 0.0000 chunk 74 optimal weight: 0.1980 chunk 245 optimal weight: 2.9990 chunk 263 optimal weight: 0.0670 chunk 191 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 303 optimal weight: 0.1980 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 ASN A1509 GLN A1760 ASN ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2099 GLN C 30 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31649 Z= 0.138 Angle : 0.520 11.608 42931 Z= 0.258 Chirality : 0.038 0.202 4953 Planarity : 0.003 0.039 5513 Dihedral : 4.081 56.626 4386 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.34 % Allowed : 17.78 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.14), residues: 3977 helix: 1.47 (0.11), residues: 2361 sheet: 0.06 (0.40), residues: 180 loop : -1.00 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A2429 HIS 0.004 0.000 HIS C 64 PHE 0.020 0.001 PHE A 306 TYR 0.030 0.001 TYR A2542 ARG 0.007 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 364 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9434 (t) cc_final: 0.9215 (p) REVERT: A 620 MET cc_start: 0.8195 (tpp) cc_final: 0.7827 (mmt) REVERT: A 679 LEU cc_start: 0.9607 (mm) cc_final: 0.9333 (tp) REVERT: A 768 ILE cc_start: 0.8252 (tp) cc_final: 0.7988 (tp) REVERT: A 772 MET cc_start: 0.8485 (mmp) cc_final: 0.8203 (mmp) REVERT: A 816 TRP cc_start: 0.8157 (m100) cc_final: 0.7907 (m100) REVERT: A 853 TYR cc_start: 0.8021 (t80) cc_final: 0.7326 (t80) REVERT: A 1108 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: A 1153 SER cc_start: 0.9171 (p) cc_final: 0.8778 (t) REVERT: A 1154 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8198 (ttt180) REVERT: A 1171 SER cc_start: 0.8119 (m) cc_final: 0.7813 (p) REVERT: A 1194 MET cc_start: 0.8727 (tmm) cc_final: 0.8216 (tmm) REVERT: A 1313 MET cc_start: 0.8694 (ppp) cc_final: 0.8246 (tmm) REVERT: A 1607 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (mm) REVERT: A 1638 MET cc_start: 0.8838 (tpp) cc_final: 0.8331 (tpp) REVERT: A 1650 MET cc_start: 0.7921 (mpp) cc_final: 0.7703 (mpp) REVERT: A 1796 MET cc_start: 0.8884 (tpp) cc_final: 0.8543 (tpt) REVERT: A 2041 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8457 (tm-30) REVERT: A 2099 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: A 2404 MET cc_start: 0.9061 (tpt) cc_final: 0.8833 (tpt) REVERT: A 2405 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8636 (mm-30) REVERT: A 2516 ASP cc_start: 0.8651 (m-30) cc_final: 0.7555 (p0) REVERT: C 118 ASN cc_start: 0.8692 (t0) cc_final: 0.8069 (t0) REVERT: C 142 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6640 (mp0) REVERT: C 143 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6674 (mp) REVERT: C 147 ASP cc_start: 0.8585 (p0) cc_final: 0.8189 (p0) REVERT: C 184 TYR cc_start: 0.8187 (m-80) cc_final: 0.7898 (m-80) REVERT: C 185 MET cc_start: 0.7309 (tmm) cc_final: 0.7000 (tmm) REVERT: C 195 TYR cc_start: 0.7238 (m-80) cc_final: 0.6733 (m-10) REVERT: C 247 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7785 (m100) REVERT: C 258 LEU cc_start: 0.7688 (mp) cc_final: 0.7362 (tt) REVERT: C 273 MET cc_start: 0.8214 (ttt) cc_final: 0.7758 (ttm) REVERT: E 81 TYR cc_start: 0.8266 (m-80) cc_final: 0.7788 (m-80) REVERT: E 124 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8032 (mmmm) REVERT: E 142 GLU cc_start: 0.7541 (tp30) cc_final: 0.7236 (tp30) REVERT: E 183 MET cc_start: 0.8741 (mtp) cc_final: 0.8537 (ttm) REVERT: E 224 ASN cc_start: 0.8754 (t0) cc_final: 0.8547 (m-40) REVERT: E 475 CYS cc_start: 0.8781 (m) cc_final: 0.8279 (m) REVERT: E 504 THR cc_start: 0.8875 (m) cc_final: 0.8664 (p) REVERT: E 545 GLU cc_start: 0.6304 (tp30) cc_final: 0.5786 (tp30) REVERT: E 561 ASN cc_start: 0.6544 (OUTLIER) cc_final: 0.5895 (t0) REVERT: E 592 ASP cc_start: 0.8426 (t0) cc_final: 0.8155 (t0) REVERT: E 675 MET cc_start: 0.8428 (mmm) cc_final: 0.8097 (tpp) REVERT: E 1642 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8285 (tptt) REVERT: G 27 CYS cc_start: 0.9042 (m) cc_final: 0.8723 (m) REVERT: I 134 MET cc_start: 0.9641 (ptt) cc_final: 0.9292 (mmm) REVERT: I 164 THR cc_start: 0.0886 (OUTLIER) cc_final: 0.0655 (p) REVERT: I 166 MET cc_start: 0.9133 (mmt) cc_final: 0.8459 (mmm) REVERT: I 212 ASN cc_start: 0.9018 (p0) cc_final: 0.8726 (t0) REVERT: I 228 MET cc_start: 0.4635 (tpt) cc_final: 0.3842 (mmt) REVERT: I 326 TYR cc_start: 0.6975 (p90) cc_final: 0.6723 (p90) REVERT: I 376 ASN cc_start: 0.9084 (p0) cc_final: 0.8371 (m-40) outliers start: 74 outliers final: 49 residues processed: 415 average time/residue: 0.3980 time to fit residues: 278.2202 Evaluate side-chains 397 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 341 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2099 GLN Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2419 GLU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 351 optimal weight: 0.2980 chunk 370 optimal weight: 20.0000 chunk 337 optimal weight: 0.9980 chunk 360 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 282 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 340 optimal weight: 0.0010 chunk 358 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2099 GLN C 30 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31649 Z= 0.153 Angle : 0.540 11.998 42931 Z= 0.265 Chirality : 0.039 0.310 4953 Planarity : 0.003 0.038 5513 Dihedral : 4.068 55.813 4386 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.96 % Allowed : 18.47 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 3977 helix: 1.52 (0.11), residues: 2353 sheet: -0.05 (0.39), residues: 190 loop : -0.99 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A2429 HIS 0.007 0.001 HIS C 64 PHE 0.011 0.001 PHE A2048 TYR 0.031 0.001 TYR A2542 ARG 0.006 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 354 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9454 (t) cc_final: 0.9223 (p) REVERT: A 620 MET cc_start: 0.8069 (tpp) cc_final: 0.7708 (mmt) REVERT: A 630 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9064 (tp) REVERT: A 679 LEU cc_start: 0.9608 (mm) cc_final: 0.9339 (tp) REVERT: A 768 ILE cc_start: 0.8308 (tp) cc_final: 0.8062 (tp) REVERT: A 816 TRP cc_start: 0.8180 (m100) cc_final: 0.7953 (m100) REVERT: A 853 TYR cc_start: 0.7994 (t80) cc_final: 0.7370 (t80) REVERT: A 1108 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: A 1153 SER cc_start: 0.9125 (p) cc_final: 0.8719 (t) REVERT: A 1171 SER cc_start: 0.8128 (m) cc_final: 0.7835 (p) REVERT: A 1194 MET cc_start: 0.8724 (tmm) cc_final: 0.8218 (tmm) REVERT: A 1231 ILE cc_start: 0.9141 (tp) cc_final: 0.8784 (tp) REVERT: A 1313 MET cc_start: 0.8703 (ppp) cc_final: 0.8256 (tmm) REVERT: A 1467 MET cc_start: 0.8197 (mmp) cc_final: 0.7861 (mmm) REVERT: A 1578 MET cc_start: 0.8555 (mmp) cc_final: 0.8296 (mmm) REVERT: A 1607 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8233 (mm) REVERT: A 1638 MET cc_start: 0.8815 (tpp) cc_final: 0.8289 (tpp) REVERT: A 1650 MET cc_start: 0.7917 (mpp) cc_final: 0.7701 (mpp) REVERT: A 1796 MET cc_start: 0.8891 (tpp) cc_final: 0.8581 (tpt) REVERT: A 2041 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8440 (tm-30) REVERT: A 2404 MET cc_start: 0.9073 (tpt) cc_final: 0.8853 (tpt) REVERT: A 2516 ASP cc_start: 0.8669 (m-30) cc_final: 0.7556 (p0) REVERT: C 86 LYS cc_start: 0.6833 (mmmt) cc_final: 0.6523 (mmmt) REVERT: C 118 ASN cc_start: 0.8696 (t0) cc_final: 0.8079 (t0) REVERT: C 142 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6649 (mp0) REVERT: C 143 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6697 (mp) REVERT: C 147 ASP cc_start: 0.8603 (p0) cc_final: 0.8241 (p0) REVERT: C 184 TYR cc_start: 0.8226 (m-80) cc_final: 0.7962 (m-80) REVERT: C 185 MET cc_start: 0.7307 (tmm) cc_final: 0.6989 (tmm) REVERT: C 195 TYR cc_start: 0.7264 (m-80) cc_final: 0.6731 (m-10) REVERT: C 247 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (m100) REVERT: C 258 LEU cc_start: 0.7748 (mp) cc_final: 0.7362 (tt) REVERT: C 273 MET cc_start: 0.8231 (ttt) cc_final: 0.7763 (ttm) REVERT: E 81 TYR cc_start: 0.8257 (m-80) cc_final: 0.7821 (m-80) REVERT: E 124 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8077 (mmmm) REVERT: E 142 GLU cc_start: 0.7568 (tp30) cc_final: 0.7252 (tp30) REVERT: E 475 CYS cc_start: 0.8780 (m) cc_final: 0.8288 (m) REVERT: E 504 THR cc_start: 0.8849 (m) cc_final: 0.8645 (p) REVERT: E 545 GLU cc_start: 0.6312 (tp30) cc_final: 0.5827 (tp30) REVERT: E 561 ASN cc_start: 0.6563 (OUTLIER) cc_final: 0.5897 (t0) REVERT: E 592 ASP cc_start: 0.8403 (t0) cc_final: 0.8117 (t0) REVERT: E 607 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8248 (tp40) REVERT: E 675 MET cc_start: 0.8422 (mmm) cc_final: 0.8108 (tpp) REVERT: E 1633 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7741 (mm-30) REVERT: E 1642 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8290 (tptt) REVERT: G 27 CYS cc_start: 0.9022 (m) cc_final: 0.8714 (m) REVERT: I 134 MET cc_start: 0.9636 (ptt) cc_final: 0.9292 (mmm) REVERT: I 164 THR cc_start: 0.0843 (OUTLIER) cc_final: 0.0627 (p) REVERT: I 166 MET cc_start: 0.9132 (mmt) cc_final: 0.8445 (mmm) REVERT: I 212 ASN cc_start: 0.9009 (p0) cc_final: 0.8725 (t0) REVERT: I 228 MET cc_start: 0.4746 (tpt) cc_final: 0.3957 (mmt) REVERT: I 326 TYR cc_start: 0.6771 (p90) cc_final: 0.6470 (p90) REVERT: I 376 ASN cc_start: 0.9095 (p0) cc_final: 0.8379 (m-40) outliers start: 62 outliers final: 48 residues processed: 395 average time/residue: 0.4123 time to fit residues: 272.0752 Evaluate side-chains 395 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 339 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2099 GLN Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2419 GLU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 236 optimal weight: 0.7980 chunk 380 optimal weight: 0.4980 chunk 232 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 399 optimal weight: 8.9990 chunk 367 optimal weight: 0.0010 chunk 318 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1077 HIS ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2099 GLN C 30 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 31649 Z= 0.180 Angle : 0.559 11.794 42931 Z= 0.274 Chirality : 0.040 0.315 4953 Planarity : 0.003 0.038 5513 Dihedral : 4.086 54.681 4386 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.00 % Allowed : 18.50 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3977 helix: 1.51 (0.11), residues: 2360 sheet: -0.06 (0.39), residues: 189 loop : -1.01 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A2429 HIS 0.011 0.001 HIS C 64 PHE 0.012 0.001 PHE A2048 TYR 0.030 0.001 TYR A2542 ARG 0.006 0.000 ARG A 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 341 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.6017 (tmm) cc_final: 0.5677 (tmm) REVERT: A 606 CYS cc_start: 0.9467 (t) cc_final: 0.9227 (p) REVERT: A 620 MET cc_start: 0.8112 (tpp) cc_final: 0.7744 (mmt) REVERT: A 630 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9051 (tp) REVERT: A 679 LEU cc_start: 0.9603 (mm) cc_final: 0.9328 (tp) REVERT: A 816 TRP cc_start: 0.8258 (m100) cc_final: 0.8029 (m100) REVERT: A 853 TYR cc_start: 0.8044 (t80) cc_final: 0.7458 (t80) REVERT: A 1108 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: A 1153 SER cc_start: 0.9125 (p) cc_final: 0.8717 (t) REVERT: A 1171 SER cc_start: 0.8109 (m) cc_final: 0.7821 (p) REVERT: A 1194 MET cc_start: 0.8729 (tmm) cc_final: 0.8227 (tmm) REVERT: A 1313 MET cc_start: 0.8695 (ppp) cc_final: 0.8254 (tmm) REVERT: A 1467 MET cc_start: 0.8256 (mmp) cc_final: 0.7837 (mmm) REVERT: A 1578 MET cc_start: 0.8606 (mmp) cc_final: 0.8339 (mmm) REVERT: A 1607 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8188 (mm) REVERT: A 1638 MET cc_start: 0.8839 (tpp) cc_final: 0.8318 (tpp) REVERT: A 1650 MET cc_start: 0.7949 (mpp) cc_final: 0.7727 (mpp) REVERT: A 1796 MET cc_start: 0.8903 (tpp) cc_final: 0.8626 (tpt) REVERT: A 2041 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8445 (tm-30) REVERT: A 2132 MET cc_start: 0.8252 (ptt) cc_final: 0.7966 (ptt) REVERT: A 2404 MET cc_start: 0.9085 (tpt) cc_final: 0.8850 (tpt) REVERT: C 86 LYS cc_start: 0.6727 (mmmt) cc_final: 0.6317 (mmmt) REVERT: C 118 ASN cc_start: 0.8710 (t0) cc_final: 0.8105 (t0) REVERT: C 142 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6629 (mp0) REVERT: C 143 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6628 (mp) REVERT: C 147 ASP cc_start: 0.8611 (p0) cc_final: 0.8346 (p0) REVERT: C 184 TYR cc_start: 0.8226 (m-80) cc_final: 0.7975 (m-80) REVERT: C 185 MET cc_start: 0.7350 (tmm) cc_final: 0.7015 (tmm) REVERT: C 247 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7771 (m100) REVERT: C 258 LEU cc_start: 0.7788 (mp) cc_final: 0.7462 (tt) REVERT: C 273 MET cc_start: 0.8265 (ttt) cc_final: 0.7906 (ttp) REVERT: E 81 TYR cc_start: 0.8292 (m-80) cc_final: 0.7850 (m-80) REVERT: E 124 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8129 (mmmm) REVERT: E 142 GLU cc_start: 0.7615 (tp30) cc_final: 0.7299 (tp30) REVERT: E 504 THR cc_start: 0.8906 (m) cc_final: 0.8687 (p) REVERT: E 545 GLU cc_start: 0.6337 (tp30) cc_final: 0.5851 (tp30) REVERT: E 561 ASN cc_start: 0.6561 (OUTLIER) cc_final: 0.5899 (t0) REVERT: E 592 ASP cc_start: 0.8409 (t0) cc_final: 0.8117 (t0) REVERT: E 675 MET cc_start: 0.8429 (mmm) cc_final: 0.8125 (tpp) REVERT: E 1607 MET cc_start: 0.5925 (mmp) cc_final: 0.5584 (mmm) REVERT: E 1642 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8294 (tptt) REVERT: G 27 CYS cc_start: 0.9000 (m) cc_final: 0.8688 (m) REVERT: I 134 MET cc_start: 0.9642 (ptt) cc_final: 0.9293 (mmm) REVERT: I 164 THR cc_start: 0.0713 (OUTLIER) cc_final: 0.0507 (p) REVERT: I 166 MET cc_start: 0.9131 (mmt) cc_final: 0.8425 (mmm) REVERT: I 212 ASN cc_start: 0.9016 (p0) cc_final: 0.8742 (t0) REVERT: I 228 MET cc_start: 0.4768 (tpt) cc_final: 0.3847 (mmt) REVERT: I 326 TYR cc_start: 0.6828 (p90) cc_final: 0.6567 (p90) REVERT: I 376 ASN cc_start: 0.9110 (p0) cc_final: 0.8396 (m-40) outliers start: 63 outliers final: 53 residues processed: 383 average time/residue: 0.4249 time to fit residues: 273.7362 Evaluate side-chains 394 residues out of total 3575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 334 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2099 GLN Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2419 GLU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 561 ASN Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 914 LEU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 29 MET Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 401 MET Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 252 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 318 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 327 optimal weight: 0.4980 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1722 GLN ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2099 GLN C 30 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN ** I 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067874 restraints weight = 97261.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070092 restraints weight = 46956.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071541 restraints weight = 29278.252| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31649 Z= 0.166 Angle : 0.562 11.782 42931 Z= 0.275 Chirality : 0.040 0.319 4953 Planarity : 0.003 0.039 5513 Dihedral : 4.096 54.458 4386 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.03 % Allowed : 18.85 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3977 helix: 1.54 (0.11), residues: 2359 sheet: -0.02 (0.39), residues: 183 loop : -0.98 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A2429 HIS 0.005 0.001 HIS C 64 PHE 0.011 0.001 PHE A2048 TYR 0.030 0.001 TYR A2542 ARG 0.009 0.000 ARG G 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7167.26 seconds wall clock time: 131 minutes 2.37 seconds (7862.37 seconds total)