Starting phenix.real_space_refine on Sat Mar 7 11:38:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ae1_11736/03_2026/7ae1_11736.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ae1_11736/03_2026/7ae1_11736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ae1_11736/03_2026/7ae1_11736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ae1_11736/03_2026/7ae1_11736.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ae1_11736/03_2026/7ae1_11736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ae1_11736/03_2026/7ae1_11736.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 286 5.16 5 C 26813 2.51 5 N 7394 2.21 5 O 8059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42608 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 10848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1381, 10848 Classifications: {'peptide': 1381} Link IDs: {'PTRANS': 65, 'TRANS': 1315} Chain breaks: 1 Chain: "B" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8680 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 2 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1001 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1509 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 849 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3211 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 23, 'TRANS': 376} Chain breaks: 1 Chain: "N" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1448 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "Q" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 883 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 12, 'TRANS': 91} Chain: "R" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "T" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 100.037 68.303 121.041 1.00 82.01 S ATOM 565 SG CYS A 72 97.803 64.602 121.311 1.00 78.11 S ATOM 613 SG CYS A 79 96.722 67.245 118.764 1.00 76.28 S ATOM 854 SG CYS A 109 67.751 96.102 145.445 1.00 89.23 S ATOM 876 SG CYS A 112 68.223 93.048 148.150 1.00 92.78 S ATOM 1245 SG CYS A 156 64.333 94.430 147.027 1.00 99.98 S ATOM 1271 SG CYS A 159 67.127 96.455 148.936 1.00102.77 S ATOM 19115 SG CYS B1080 83.898 62.195 130.250 1.00 70.89 S ATOM 19134 SG CYS B1083 83.588 66.109 130.431 1.00 70.04 S ATOM 19200 SG CYS B1092 87.099 64.603 130.303 1.00 74.21 S ATOM 19228 SG CYS B1095 84.949 64.272 133.564 1.00 73.49 S ATOM 28343 SG CYS I 5 56.619 148.392 110.263 1.00 78.98 S ATOM 28360 SG CYS I 8 60.184 146.548 111.501 1.00 77.78 S ATOM 28491 SG CYS I 25 57.456 145.140 113.450 1.00 86.19 S ATOM 28512 SG CYS I 28 57.817 148.799 113.601 1.00 87.33 S ATOM 29206 SG CYS J 7 88.941 75.086 49.195 1.00 34.75 S ATOM 29230 SG CYS J 10 88.220 72.315 46.454 1.00 33.88 S ATOM 29494 SG CYS J 44 85.380 75.292 47.148 1.00 37.43 S ATOM 29500 SG CYS J 45 88.901 75.586 45.103 1.00 38.78 S ATOM 30589 SG CYS L 19 122.214 91.574 71.588 1.00 64.11 S ATOM 30608 SG CYS L 22 123.970 93.129 68.888 1.00 69.60 S ATOM 30725 SG CYS L 36 125.799 92.258 72.308 1.00 72.97 S Time building chain proxies: 8.91, per 1000 atoms: 0.21 Number of scatterers: 42608 At special positions: 0 Unit cell: (141.75, 183.75, 206.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 286 16.00 P 44 15.00 Mg 1 11.99 O 8059 8.00 N 7394 7.00 C 26813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 296 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 24 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9870 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 57 sheets defined 41.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.788A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.502A pdb=" N GLY A 61 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.674A pdb=" N GLY A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.521A pdb=" N ASP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 3.544A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.531A pdb=" N PHE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.806A pdb=" N HIS A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.771A pdb=" N LEU A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.918A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.676A pdb=" N ILE A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.911A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.715A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.824A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 546 through 553 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.922A pdb=" N ASP A 576 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 4.226A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.585A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 695 removed outlier: 3.554A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.790A pdb=" N ASN A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 removed outlier: 3.829A pdb=" N ALA A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 771 removed outlier: 3.947A pdb=" N ARG A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 828 through 832 removed outlier: 3.925A pdb=" N GLY A 832 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.668A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N MET A 871 " --> pdb=" O GLU A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.529A pdb=" N MET A 912 " --> pdb=" O PRO A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 953 Processing helix chain 'A' and resid 955 through 961 removed outlier: 3.716A pdb=" N CYS A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 988 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1024 Processing helix chain 'A' and resid 1032 through 1048 Proline residue: A1044 - end of helix removed outlier: 3.772A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.699A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.721A pdb=" N ALA A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1100 " --> pdb=" O ASP A1096 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1145 through 1153 removed outlier: 4.010A pdb=" N TYR A1151 " --> pdb=" O GLU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 4.119A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 removed outlier: 3.611A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.876A pdb=" N THR A1246 " --> pdb=" O GLY A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 Processing helix chain 'A' and resid 1259 through 1278 removed outlier: 3.513A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 removed outlier: 4.065A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1319 Processing helix chain 'A' and resid 1323 through 1335 removed outlier: 3.980A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 3.696A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1359' Processing helix chain 'A' and resid 1381 through 1385 removed outlier: 3.552A pdb=" N PHE A1384 " --> pdb=" O THR A1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 35 Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.962A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.630A pdb=" N CYS B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.624A pdb=" N ALA B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 273 Proline residue: B 267 - end of helix removed outlier: 3.610A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.911A pdb=" N LEU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 347 removed outlier: 3.868A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.907A pdb=" N LEU B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 5.651A pdb=" N ARG B 407 " --> pdb=" O LYS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 427 through 430 removed outlier: 3.541A pdb=" N LYS B 430 " --> pdb=" O LYS B 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 444 through 452 removed outlier: 3.538A pdb=" N ALA B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 516 removed outlier: 4.173A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.616A pdb=" N LEU B 526 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.554A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 616 Processing helix chain 'B' and resid 620 through 627 removed outlier: 3.587A pdb=" N PHE B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.908A pdb=" N ASN B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 3.940A pdb=" N GLU B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 803 through 807 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.659A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 954 removed outlier: 3.763A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.888A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1019 Processing helix chain 'B' and resid 1048 through 1058 removed outlier: 3.527A pdb=" N ASP B1053 " --> pdb=" O GLU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 removed outlier: 4.183A pdb=" N GLN B1118 " --> pdb=" O PHE B1114 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 removed outlier: 4.227A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.567A pdb=" N LEU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.619A pdb=" N PHE C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.817A pdb=" N GLU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.509A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.882A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.788A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 4.233A pdb=" N GLN D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 124 removed outlier: 3.607A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.681A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 removed outlier: 4.815A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.911A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.897A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.663A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 Processing helix chain 'G' and resid 199 through 201 No H-bonds generated for 'chain 'G' and resid 199 through 201' Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.508A pdb=" N LEU I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY I 54 " --> pdb=" O ASP I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 54' Processing helix chain 'J' and resid 17 through 25 removed outlier: 3.718A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 3.684A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.103A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 63 removed outlier: 4.772A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 61 removed outlier: 4.020A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 128 Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.608A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 154 removed outlier: 3.748A pdb=" N ASP M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 201 Processing helix chain 'M' and resid 215 through 222 removed outlier: 3.618A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 226 Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 277 through 289 removed outlier: 3.511A pdb=" N GLN M 281 " --> pdb=" O PRO M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 310 through 315 Processing helix chain 'M' and resid 328 through 333 removed outlier: 4.150A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 363 removed outlier: 4.485A pdb=" N VAL M 356 " --> pdb=" O GLY M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 375 removed outlier: 3.781A pdb=" N VAL M 374 " --> pdb=" O GLU M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 386 removed outlier: 4.003A pdb=" N ASP M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 410 removed outlier: 4.120A pdb=" N ILE M 409 " --> pdb=" O GLY M 406 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS M 410 " --> pdb=" O GLU M 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 406 through 410' Processing helix chain 'M' and resid 414 through 431 removed outlier: 4.548A pdb=" N HIS M 420 " --> pdb=" O VAL M 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 124 removed outlier: 3.957A pdb=" N TRP N 123 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.884A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 257 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 388 through 396 removed outlier: 4.247A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 18 through 32 removed outlier: 4.832A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 42 removed outlier: 3.591A pdb=" N ALA O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 84 Processing helix chain 'O' and resid 87 through 99 removed outlier: 3.577A pdb=" N LYS O 96 " --> pdb=" O ILE O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 114 removed outlier: 3.596A pdb=" N VAL O 107 " --> pdb=" O GLY O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 129 Processing helix chain 'O' and resid 141 through 154 removed outlier: 4.038A pdb=" N THR O 147 " --> pdb=" O GLU O 143 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG O 150 " --> pdb=" O ASN O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 removed outlier: 3.628A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 275 Processing helix chain 'O' and resid 290 through 297 removed outlier: 4.284A pdb=" N ARG O 295 " --> pdb=" O ASN O 291 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER O 296 " --> pdb=" O GLU O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 337 through 359 removed outlier: 3.527A pdb=" N VAL O 354 " --> pdb=" O LEU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 372 removed outlier: 3.555A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 385 Processing helix chain 'O' and resid 390 through 401 Processing helix chain 'O' and resid 416 through 418 No H-bonds generated for 'chain 'O' and resid 416 through 418' Processing helix chain 'O' and resid 427 through 456 removed outlier: 3.566A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 removed outlier: 3.620A pdb=" N GLU O 468 " --> pdb=" O SER O 464 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.890A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 531 removed outlier: 4.320A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU O 522 " --> pdb=" O GLU O 518 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET O 531 " --> pdb=" O ILE O 527 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.777A pdb=" N GLU P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 removed outlier: 3.614A pdb=" N PHE P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 224 removed outlier: 3.832A pdb=" N TRP P 217 " --> pdb=" O SER P 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU P 222 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY P 224 " --> pdb=" O ILE P 220 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 239 removed outlier: 4.354A pdb=" N THR P 237 " --> pdb=" O GLU P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 245 removed outlier: 3.632A pdb=" N ILE P 243 " --> pdb=" O LEU P 239 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 285 removed outlier: 3.994A pdb=" N ARG P 284 " --> pdb=" O THR P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 290 Processing helix chain 'P' and resid 292 through 296 removed outlier: 3.522A pdb=" N CYS P 296 " --> pdb=" O PHE P 293 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 306 Processing helix chain 'P' and resid 307 through 314 Processing helix chain 'Q' and resid 15 through 20 removed outlier: 3.885A pdb=" N VAL Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 69 removed outlier: 3.778A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU Q 66 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.964A pdb=" N ARG Q 90 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.515A pdb=" N MET Q 110 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET Q 111 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 107 through 111' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.863A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ARG G 73 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP G 50 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR G 52 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N LYS G 69 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N LEU G 54 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N HIS G 67 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.863A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ARG G 73 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP G 50 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR G 52 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N LYS G 69 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N LEU G 54 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N HIS G 67 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE G 2 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 6.921A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B1123 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.766A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 88 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N ILE A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.926A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 359 through 361 removed outlier: 3.502A pdb=" N LEU B1045 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 3.885A pdb=" N PHE A 488 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.042A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 616 through 620 removed outlier: 6.456A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.518A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1209 through 1214 removed outlier: 3.830A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 7.439A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1165 through 1169 removed outlier: 3.861A pdb=" N HIS A1168 " --> pdb=" O VAL A1172 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1172 " --> pdb=" O HIS A1168 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.474A pdb=" N LEU A1362 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 66 removed outlier: 7.033A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.749A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'B' and resid 360 through 363 removed outlier: 3.610A pdb=" N ILE B 180 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.806A pdb=" N THR B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 424 through 426 removed outlier: 4.332A pdb=" N ARG B 433 " --> pdb=" O TRP B 424 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC5, first strand: chain 'B' and resid 603 through 604 Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 549 removed outlier: 6.566A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 537 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.801A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.801A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 720 through 721 Processing sheet with id=AD1, first strand: chain 'B' and resid 986 through 987 removed outlier: 6.646A pdb=" N LEU B 755 " --> pdb=" O LEU B 909 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL B 911 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 757 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.246A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.521A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.868A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.739A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 174 through 175 removed outlier: 3.686A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AD9, first strand: chain 'C' and resid 167 through 169 removed outlier: 7.071A pdb=" N VAL C 168 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.667A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE3, first strand: chain 'E' and resid 62 through 63 removed outlier: 5.748A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.956A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.824A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 196 through 197 removed outlier: 5.423A pdb=" N VAL G 152 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER G 189 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N PHE G 104 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU G 186 " --> pdb=" O PHE G 104 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP G 106 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY G 188 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU G 108 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP G 106 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL G 99 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU G 108 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 128 through 129 removed outlier: 4.002A pdb=" N ASP G 139 " --> pdb=" O TRP G 129 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.737A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF2, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.713A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 27 through 31 removed outlier: 3.520A pdb=" N GLU K 28 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LYS K 79 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR K 72 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN K 81 " --> pdb=" O TYR K 70 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR K 70 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG K 83 " --> pdb=" O CYS K 68 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS K 68 " --> pdb=" O ARG K 83 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN K 85 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 370 through 387 removed outlier: 6.919A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU N 357 " --> pdb=" O TYR M 30 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE N 356 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS N 380 " --> pdb=" O PHE N 356 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU N 266 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU M 124 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP M 14 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU M 126 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR M 16 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 291 through 292 removed outlier: 3.537A pdb=" N MET M 292 " --> pdb=" O TRP M 325 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 390 through 392 Processing sheet with id=AF7, first strand: chain 'O' and resid 34 through 35 Processing sheet with id=AF8, first strand: chain 'O' and resid 116 through 117 Processing sheet with id=AF9, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AG1, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AG2, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AG3, first strand: chain 'P' and resid 211 through 212 1717 hydrogen bonds defined for protein. 4749 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: 10.48 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 17803 1.43 - 1.64: 25236 1.64 - 1.86: 446 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 43497 Sorted by residual: bond pdb=" C GLN G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.334 1.379 -0.045 1.51e-02 4.39e+03 8.83e+00 bond pdb=" CA LYS A1182 " pdb=" CB LYS A1182 " ideal model delta sigma weight residual 1.521 1.554 -0.034 1.48e-02 4.57e+03 5.16e+00 bond pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.27e-02 6.20e+03 4.52e+00 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.52e+00 bond pdb=" CA ILE N 284 " pdb=" CB ILE N 284 " ideal model delta sigma weight residual 1.540 1.597 -0.057 2.70e-02 1.37e+03 4.44e+00 ... (remaining 43492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 57748 3.09 - 6.18: 1051 6.18 - 9.26: 98 9.26 - 12.35: 20 12.35 - 15.44: 4 Bond angle restraints: 58921 Sorted by residual: angle pdb=" C LEU B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 121.97 135.14 -13.17 1.80e+00 3.09e-01 5.36e+01 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" CB VAL B 40 " ideal model delta sigma weight residual 111.23 102.51 8.72 1.65e+00 3.67e-01 2.79e+01 angle pdb=" C VAL M 262 " pdb=" N ALA M 263 " pdb=" CA ALA M 263 " ideal model delta sigma weight residual 121.80 134.63 -12.83 2.44e+00 1.68e-01 2.77e+01 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 120.13 -10.79 2.08e+00 2.31e-01 2.69e+01 angle pdb=" C ASP E 2 " pdb=" N ASP E 3 " pdb=" CA ASP E 3 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 ... (remaining 58916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.34: 26085 30.34 - 60.69: 520 60.69 - 91.03: 32 91.03 - 121.37: 0 121.37 - 151.71: 2 Dihedral angle restraints: 26639 sinusoidal: 11374 harmonic: 15265 Sorted by residual: dihedral pdb=" CA LEU B 39 " pdb=" C LEU B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta harmonic sigma weight residual -180.00 -139.88 -40.12 0 5.00e+00 4.00e-02 6.44e+01 dihedral pdb=" CA LYS A 580 " pdb=" C LYS A 580 " pdb=" N VAL A 581 " pdb=" CA VAL A 581 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ARG N 145 " pdb=" C ARG N 145 " pdb=" N GLU N 146 " pdb=" CA GLU N 146 " ideal model delta harmonic sigma weight residual 180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 26636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5161 0.072 - 0.143: 1249 0.143 - 0.215: 178 0.215 - 0.286: 21 0.286 - 0.358: 12 Chirality restraints: 6621 Sorted by residual: chirality pdb=" CB ILE A 473 " pdb=" CA ILE A 473 " pdb=" CG1 ILE A 473 " pdb=" CG2 ILE A 473 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB ILE A 542 " pdb=" CA ILE A 542 " pdb=" CG1 ILE A 542 " pdb=" CG2 ILE A 542 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB VAL A1058 " pdb=" CA VAL A1058 " pdb=" CG1 VAL A1058 " pdb=" CG2 VAL A1058 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 6618 not shown) Planarity restraints: 7442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 357 " 0.025 2.00e-02 2.50e+03 2.34e-02 1.09e+01 pdb=" CG TYR B 357 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 357 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 357 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 357 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 357 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 357 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 357 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 194 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C HIS C 194 " -0.055 2.00e-02 2.50e+03 pdb=" O HIS C 194 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP C 195 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 629 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C GLU A 629 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU A 629 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 630 " -0.018 2.00e-02 2.50e+03 ... (remaining 7439 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 5 2.28 - 2.94: 16413 2.94 - 3.59: 57299 3.59 - 4.25: 95696 4.25 - 4.90: 161256 Nonbonded interactions: 330669 Sorted by model distance: nonbonded pdb=" O3' G R 19 " pdb="MG MG R 101 " model vdw 1.628 2.170 nonbonded pdb=" OD1 ASP A 501 " pdb="MG MG R 101 " model vdw 1.887 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG R 101 " model vdw 2.261 2.170 nonbonded pdb=" OD1 ASP A 503 " pdb=" O2' G R 19 " model vdw 2.263 3.040 nonbonded pdb=" OG SER H 32 " pdb=" O PHE H 35 " model vdw 2.266 3.040 ... (remaining 330664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 47.350 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.090 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:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.011 0.791 43523 Z= 0.394 Angle : 1.156 49.819 58957 Z= 0.587 Chirality : 0.064 0.358 6621 Planarity : 0.007 0.073 7442 Dihedral : 12.184 151.713 16769 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 0.45 % Allowed : 3.89 % Favored : 95.66 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.10), residues: 5193 helix: -2.06 (0.10), residues: 1794 sheet: -0.18 (0.19), residues: 652 loop : -1.05 (0.11), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.004 ARG C 78 TYR 0.058 0.004 TYR B 357 PHE 0.046 0.004 PHE A 462 TRP 0.030 0.003 TRP I 59 HIS 0.014 0.002 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00769 (43497) covalent geometry : angle 1.05496 (58921) hydrogen bonds : bond 0.26041 ( 1679) hydrogen bonds : angle 8.11377 ( 4749) metal coordination : bond 0.32904 ( 26) metal coordination : angle 19.17053 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 465 time to evaluate : 1.620 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: D 18 GLN cc_start: 0.8772 (tt0) cc_final: 0.8366 (tp40) REVERT: D 26 GLN cc_start: 0.8540 (pp30) cc_final: 0.8318 (pp30) REVERT: D 100 MET cc_start: 0.7819 (mtt) cc_final: 0.7617 (mtm) REVERT: G 119 LYS cc_start: 0.7669 (mttm) cc_final: 0.7379 (mmmm) REVERT: G 140 LEU cc_start: 0.7794 (pt) cc_final: 0.7545 (mt) REVERT: I 91 MET cc_start: 0.4732 (mtp) cc_final: 0.4101 (mmm) REVERT: J 1 MET cc_start: 0.8295 (ttm) cc_final: 0.7993 (ttm) REVERT: K 119 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8226 (ttpp) REVERT: M 339 SER cc_start: -0.2454 (OUTLIER) cc_final: -0.2716 (t) REVERT: M 357 MET cc_start: 0.4640 (mpp) cc_final: 0.4053 (tmm) REVERT: P 203 MET cc_start: 0.8402 (tpt) cc_final: 0.8017 (tpt) REVERT: P 207 ASN cc_start: 0.8957 (m110) cc_final: 0.8502 (m110) REVERT: P 267 MET cc_start: 0.6818 (tpt) cc_final: 0.6518 (tpt) REVERT: P 268 LYS cc_start: 0.8760 (mttt) cc_final: 0.8441 (mppt) REVERT: P 270 TYR cc_start: 0.8079 (m-80) cc_final: 0.7653 (m-80) REVERT: Q 92 MET cc_start: 0.7815 (mtt) cc_final: 0.7544 (ppp) REVERT: Q 96 LYS cc_start: 0.6823 (tptt) cc_final: 0.6335 (tppp) outliers start: 21 outliers final: 6 residues processed: 485 average time/residue: 0.9437 time to fit residues: 537.4015 Evaluate side-chains 287 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 280 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain M residue 339 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 40.0000 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 9.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.0270 chunk 516 optimal weight: 10.0000 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 419 ASN A 476 HIS A 616 ASN A 662 ASN A 693 ASN A 791 ASN A 836 ASN A 927 ASN B 183 GLN B 215 ASN B 320 HIS B 346 GLN B 602 GLN B 683 ASN B 758 ASN ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 932 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 26 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS H 76 ASN I 40 ASN ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN J 61 ASN K 74 HIS K 85 GLN L 23 HIS M 125 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS N 111 GLN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS O 457 ASN O 515 GLN P 181 ASN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.080160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.050272 restraints weight = 132683.407| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.78 r_work: 0.2783 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43523 Z= 0.158 Angle : 0.666 18.351 58957 Z= 0.341 Chirality : 0.044 0.183 6621 Planarity : 0.005 0.073 7442 Dihedral : 10.184 156.251 6198 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.62 % Favored : 97.36 % Rotamer: Outliers : 1.56 % Allowed : 8.57 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.11), residues: 5193 helix: -0.31 (0.12), residues: 1867 sheet: -0.09 (0.19), residues: 695 loop : -0.73 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 70 TYR 0.023 0.001 TYR H 90 PHE 0.021 0.001 PHE A 462 TRP 0.017 0.001 TRP G 16 HIS 0.015 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00357 (43497) covalent geometry : angle 0.64727 (58921) hydrogen bonds : bond 0.05161 ( 1679) hydrogen bonds : angle 5.06988 ( 4749) metal coordination : bond 0.00991 ( 26) metal coordination : angle 6.34853 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 303 time to evaluate : 1.462 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: B 384 MET cc_start: 0.8471 (tpt) cc_final: 0.8223 (tpt) REVERT: B 427 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8984 (pptt) REVERT: D 5 ASP cc_start: 0.8130 (t0) cc_final: 0.7696 (t0) REVERT: D 18 GLN cc_start: 0.9108 (tt0) cc_final: 0.8696 (pt0) REVERT: D 26 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8806 (pp30) REVERT: E 152 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7902 (p) REVERT: F 125 ILE cc_start: 0.9289 (pp) cc_final: 0.8955 (mp) REVERT: G 120 PHE cc_start: 0.6799 (m-80) cc_final: 0.6221 (p90) REVERT: I 45 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8288 (tppt) REVERT: I 91 MET cc_start: 0.5029 (mtp) cc_final: 0.4410 (mmm) REVERT: J 1 MET cc_start: 0.9092 (ttm) cc_final: 0.8708 (ttm) REVERT: K 124 GLN cc_start: 0.8177 (tm130) cc_final: 0.7868 (tm-30) REVERT: L 15 MET cc_start: 0.8694 (mmm) cc_final: 0.8398 (mmm) REVERT: L 21 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: L 44 MET cc_start: 0.9351 (mmt) cc_final: 0.9001 (mmt) REVERT: M 123 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: M 270 MET cc_start: 0.5082 (OUTLIER) cc_final: 0.4621 (mpt) REVERT: M 339 SER cc_start: 0.0362 (OUTLIER) cc_final: -0.0795 (t) REVERT: M 357 MET cc_start: 0.3509 (mpp) cc_final: 0.2893 (ttt) REVERT: P 203 MET cc_start: 0.9056 (tpt) cc_final: 0.8583 (tpp) REVERT: P 207 ASN cc_start: 0.9041 (m110) cc_final: 0.8404 (m110) REVERT: P 268 LYS cc_start: 0.9303 (mttt) cc_final: 0.8701 (mppt) REVERT: Q 92 MET cc_start: 0.8097 (mtt) cc_final: 0.7760 (ppp) REVERT: Q 96 LYS cc_start: 0.6901 (tptt) cc_final: 0.6214 (tppp) REVERT: Q 108 ARG cc_start: 0.9044 (ptm160) cc_final: 0.8513 (ptm160) REVERT: Q 111 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8445 (mpp) outliers start: 72 outliers final: 18 residues processed: 353 average time/residue: 0.8104 time to fit residues: 344.5559 Evaluate side-chains 295 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain Q residue 111 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 250 optimal weight: 6.9990 chunk 412 optimal weight: 0.9990 chunk 325 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 410 optimal weight: 30.0000 chunk 478 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 469 optimal weight: 20.0000 chunk 365 optimal weight: 0.8980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 158 HIS A 182 ASN A 316 GLN ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 HIS C 305 HIS D 7 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 278 GLN O 60 HIS ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.078413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047768 restraints weight = 134592.024| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.88 r_work: 0.2718 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 43523 Z= 0.232 Angle : 0.643 13.005 58957 Z= 0.329 Chirality : 0.045 0.185 6621 Planarity : 0.005 0.058 7442 Dihedral : 10.009 156.948 6196 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.90 % Rotamer: Outliers : 1.88 % Allowed : 8.83 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.11), residues: 5193 helix: 0.28 (0.12), residues: 1897 sheet: -0.08 (0.19), residues: 704 loop : -0.70 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 85 TYR 0.033 0.002 TYR B 357 PHE 0.021 0.002 PHE A 462 TRP 0.018 0.001 TRP N 123 HIS 0.015 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00550 (43497) covalent geometry : angle 0.63298 (58921) hydrogen bonds : bond 0.04812 ( 1679) hydrogen bonds : angle 4.75216 ( 4749) metal coordination : bond 0.00952 ( 26) metal coordination : angle 4.58785 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 280 time to evaluate : 1.808 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: B 611 MET cc_start: 0.9330 (mmm) cc_final: 0.9107 (mmm) REVERT: C 330 MET cc_start: 0.8994 (mtp) cc_final: 0.8727 (mtt) REVERT: D 5 ASP cc_start: 0.7936 (t0) cc_final: 0.7238 (t0) REVERT: D 18 GLN cc_start: 0.9033 (tt0) cc_final: 0.8791 (pt0) REVERT: D 22 ASP cc_start: 0.9070 (m-30) cc_final: 0.8819 (p0) REVERT: D 26 GLN cc_start: 0.9247 (pp30) cc_final: 0.8947 (pp30) REVERT: D 67 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8434 (mmt-90) REVERT: D 114 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8938 (mm-30) REVERT: E 152 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7928 (p) REVERT: G 120 PHE cc_start: 0.7036 (m-80) cc_final: 0.6370 (p90) REVERT: I 91 MET cc_start: 0.5346 (mtp) cc_final: 0.4654 (mmm) REVERT: J 1 MET cc_start: 0.9072 (ttm) cc_final: 0.8674 (ttm) REVERT: J 57 GLU cc_start: 0.9156 (tp30) cc_final: 0.8944 (mm-30) REVERT: L 30 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8008 (p) REVERT: L 44 MET cc_start: 0.9446 (mmt) cc_final: 0.9072 (mmt) REVERT: M 247 MET cc_start: 0.8936 (tpp) cc_final: 0.8631 (tpt) REVERT: M 270 MET cc_start: 0.5073 (mpt) cc_final: 0.4593 (mpt) REVERT: M 357 MET cc_start: 0.3502 (mpp) cc_final: 0.2829 (ttp) REVERT: N 115 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: P 203 MET cc_start: 0.9127 (tpt) cc_final: 0.8503 (tpp) REVERT: P 207 ASN cc_start: 0.9032 (m110) cc_final: 0.8313 (m-40) REVERT: P 268 LYS cc_start: 0.9257 (mttt) cc_final: 0.8768 (mppt) REVERT: Q 37 LEU cc_start: 0.8251 (mp) cc_final: 0.7903 (pt) REVERT: Q 70 ARG cc_start: 0.8883 (mtm110) cc_final: 0.8622 (mtm110) REVERT: Q 92 MET cc_start: 0.8115 (mtt) cc_final: 0.7659 (ppp) REVERT: Q 96 LYS cc_start: 0.6974 (tptt) cc_final: 0.6319 (tppp) REVERT: Q 108 ARG cc_start: 0.9068 (ptm160) cc_final: 0.8506 (ptm160) outliers start: 87 outliers final: 32 residues processed: 343 average time/residue: 0.8189 time to fit residues: 338.6015 Evaluate side-chains 303 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 331 ILE Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain Q residue 60 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 469 optimal weight: 0.7980 chunk 394 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 508 optimal weight: 0.0470 chunk 260 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 404 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 434 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 500 optimal weight: 0.8980 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 GLN P 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.079524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048746 restraints weight = 134426.057| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.85 r_work: 0.2755 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43523 Z= 0.119 Angle : 0.567 11.179 58957 Z= 0.287 Chirality : 0.042 0.168 6621 Planarity : 0.004 0.057 7442 Dihedral : 9.859 157.322 6195 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 1.45 % Allowed : 10.17 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.11), residues: 5193 helix: 0.67 (0.12), residues: 1888 sheet: 0.09 (0.19), residues: 695 loop : -0.57 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 70 TYR 0.019 0.001 TYR Q 87 PHE 0.015 0.001 PHE A 462 TRP 0.021 0.001 TRP N 123 HIS 0.008 0.001 HIS I 21 Details of bonding type rmsd covalent geometry : bond 0.00270 (43497) covalent geometry : angle 0.55974 (58921) hydrogen bonds : bond 0.03764 ( 1679) hydrogen bonds : angle 4.46444 ( 4749) metal coordination : bond 0.00536 ( 26) metal coordination : angle 3.71715 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 1.374 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: B 431 MET cc_start: 0.8690 (ttt) cc_final: 0.8312 (ttm) REVERT: B 791 MET cc_start: 0.8758 (mmt) cc_final: 0.8555 (mmm) REVERT: B 854 VAL cc_start: 0.9388 (OUTLIER) cc_final: 0.9171 (m) REVERT: C 330 MET cc_start: 0.8941 (mtp) cc_final: 0.8687 (mtt) REVERT: D 5 ASP cc_start: 0.7824 (t0) cc_final: 0.7158 (t0) REVERT: D 18 GLN cc_start: 0.8999 (tt0) cc_final: 0.8752 (pt0) REVERT: D 26 GLN cc_start: 0.9268 (pp30) cc_final: 0.8937 (pp30) REVERT: D 112 GLN cc_start: 0.8622 (mt0) cc_final: 0.8350 (pt0) REVERT: F 84 GLU cc_start: 0.8517 (pp20) cc_final: 0.8213 (pp20) REVERT: F 86 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: G 120 PHE cc_start: 0.6973 (m-80) cc_final: 0.6326 (p90) REVERT: H 37 MET cc_start: 0.8830 (mmt) cc_final: 0.8579 (mmt) REVERT: I 42 LYS cc_start: 0.9394 (mmmm) cc_final: 0.8752 (tppt) REVERT: I 91 MET cc_start: 0.5352 (mtp) cc_final: 0.4605 (mmm) REVERT: J 1 MET cc_start: 0.9044 (ttm) cc_final: 0.8659 (ttm) REVERT: L 30 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8185 (p) REVERT: L 42 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8860 (mtp180) REVERT: L 44 MET cc_start: 0.9425 (mmt) cc_final: 0.9097 (mmt) REVERT: M 123 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: M 247 MET cc_start: 0.8937 (tpp) cc_final: 0.8647 (tmm) REVERT: M 270 MET cc_start: 0.4811 (mpt) cc_final: 0.4330 (mpt) REVERT: M 357 MET cc_start: 0.3328 (mpp) cc_final: 0.2750 (ttm) REVERT: N 115 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: O 118 MET cc_start: 0.9226 (ttm) cc_final: 0.8762 (mtm) REVERT: P 203 MET cc_start: 0.9114 (tpt) cc_final: 0.8467 (tpp) REVERT: P 207 ASN cc_start: 0.9036 (m110) cc_final: 0.8279 (m110) REVERT: P 268 LYS cc_start: 0.9362 (mttt) cc_final: 0.8815 (mppt) REVERT: Q 70 ARG cc_start: 0.8969 (mtm110) cc_final: 0.8734 (mtm110) REVERT: Q 92 MET cc_start: 0.8088 (mtt) cc_final: 0.7624 (ppp) REVERT: Q 96 LYS cc_start: 0.6954 (tptt) cc_final: 0.6301 (tppp) REVERT: Q 108 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8635 (ptm160) outliers start: 67 outliers final: 23 residues processed: 328 average time/residue: 0.8136 time to fit residues: 321.1918 Evaluate side-chains 293 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 189 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 148 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 373 optimal weight: 7.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN G 98 HIS ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.079787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049784 restraints weight = 135218.867| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.81 r_work: 0.2734 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43523 Z= 0.166 Angle : 0.576 12.195 58957 Z= 0.290 Chirality : 0.043 0.171 6621 Planarity : 0.004 0.053 7442 Dihedral : 9.801 157.205 6195 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.75 % Rotamer: Outliers : 1.51 % Allowed : 10.58 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 5193 helix: 0.90 (0.12), residues: 1891 sheet: -0.05 (0.19), residues: 720 loop : -0.53 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 125 TYR 0.028 0.001 TYR Q 87 PHE 0.015 0.001 PHE A 462 TRP 0.030 0.001 TRP N 123 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00391 (43497) covalent geometry : angle 0.56799 (58921) hydrogen bonds : bond 0.03775 ( 1679) hydrogen bonds : angle 4.40502 ( 4749) metal coordination : bond 0.00767 ( 26) metal coordination : angle 3.82826 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 1.617 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 332 MET cc_start: 0.7666 (mmm) cc_final: 0.7296 (mmp) REVERT: B 791 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: B 854 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9226 (m) REVERT: D 5 ASP cc_start: 0.7965 (t0) cc_final: 0.7274 (t0) REVERT: D 18 GLN cc_start: 0.9011 (tt0) cc_final: 0.8788 (pt0) REVERT: D 26 GLN cc_start: 0.9269 (pp30) cc_final: 0.8955 (pp30) REVERT: D 112 GLN cc_start: 0.8629 (mt0) cc_final: 0.8420 (pt0) REVERT: E 152 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7786 (p) REVERT: G 120 PHE cc_start: 0.6945 (m-80) cc_final: 0.6455 (p90) REVERT: H 37 MET cc_start: 0.8969 (mmt) cc_final: 0.8698 (mmt) REVERT: H 92 MET cc_start: 0.9384 (mtp) cc_final: 0.9170 (mtm) REVERT: I 91 MET cc_start: 0.5390 (mtp) cc_final: 0.4503 (tpp) REVERT: J 1 MET cc_start: 0.9069 (ttm) cc_final: 0.8718 (ttm) REVERT: K 124 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8140 (tm-30) REVERT: L 30 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8369 (p) REVERT: L 44 MET cc_start: 0.9457 (mmt) cc_final: 0.9109 (mmt) REVERT: M 123 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: M 247 MET cc_start: 0.8987 (tpp) cc_final: 0.8649 (tmm) REVERT: M 270 MET cc_start: 0.4725 (mpt) cc_final: 0.4196 (mpt) REVERT: M 357 MET cc_start: 0.3229 (mpp) cc_final: 0.2643 (ttm) REVERT: N 115 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: O 31 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9244 (p) REVERT: O 118 MET cc_start: 0.9260 (ttm) cc_final: 0.8641 (mtm) REVERT: O 133 MET cc_start: 0.4658 (ptt) cc_final: 0.4066 (pmt) REVERT: O 531 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7543 (tpt) REVERT: P 203 MET cc_start: 0.9068 (tpt) cc_final: 0.8396 (tpp) REVERT: P 207 ASN cc_start: 0.9039 (m110) cc_final: 0.8255 (m-40) REVERT: P 268 LYS cc_start: 0.9313 (mttt) cc_final: 0.8815 (mppt) REVERT: Q 37 LEU cc_start: 0.8258 (mp) cc_final: 0.7853 (pt) REVERT: Q 92 MET cc_start: 0.7912 (mtt) cc_final: 0.7490 (ppp) REVERT: Q 96 LYS cc_start: 0.6915 (tptt) cc_final: 0.6238 (tppp) outliers start: 70 outliers final: 31 residues processed: 323 average time/residue: 0.7856 time to fit residues: 307.9759 Evaluate side-chains 297 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 791 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 495 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 363 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 325 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 423 optimal weight: 8.9990 chunk 493 optimal weight: 8.9990 chunk 412 optimal weight: 0.0030 chunk 218 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS G 98 HIS K 38 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.078193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.047303 restraints weight = 134526.560| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.91 r_work: 0.2704 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43523 Z= 0.201 Angle : 0.594 12.254 58957 Z= 0.299 Chirality : 0.043 0.178 6621 Planarity : 0.004 0.061 7442 Dihedral : 9.792 156.861 6194 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 1.60 % Allowed : 10.95 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 5193 helix: 1.00 (0.12), residues: 1901 sheet: -0.10 (0.19), residues: 720 loop : -0.54 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Q 70 TYR 0.033 0.001 TYR Q 87 PHE 0.025 0.001 PHE A1384 TRP 0.028 0.001 TRP N 123 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00474 (43497) covalent geometry : angle 0.58617 (58921) hydrogen bonds : bond 0.03852 ( 1679) hydrogen bonds : angle 4.41131 ( 4749) metal coordination : bond 0.00925 ( 26) metal coordination : angle 3.96378 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 273 time to evaluate : 1.669 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7780 (mmm) cc_final: 0.7447 (mmp) REVERT: B 427 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8978 (mmmt) REVERT: B 431 MET cc_start: 0.8615 (ttt) cc_final: 0.8094 (ttm) REVERT: B 791 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8571 (mmm) REVERT: D 5 ASP cc_start: 0.8033 (t0) cc_final: 0.7350 (t0) REVERT: D 18 GLN cc_start: 0.9070 (tt0) cc_final: 0.8734 (pt0) REVERT: D 26 GLN cc_start: 0.9305 (pp30) cc_final: 0.9008 (pp30) REVERT: D 67 ARG cc_start: 0.8864 (mmt180) cc_final: 0.8606 (mmt-90) REVERT: E 152 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7871 (p) REVERT: G 120 PHE cc_start: 0.7099 (m-80) cc_final: 0.6582 (p90) REVERT: I 80 MET cc_start: 0.7198 (tpp) cc_final: 0.6693 (mtt) REVERT: I 91 MET cc_start: 0.5545 (mtp) cc_final: 0.4831 (mmm) REVERT: J 1 MET cc_start: 0.9131 (ttm) cc_final: 0.8858 (ttm) REVERT: K 124 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8135 (tm-30) REVERT: K 128 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7839 (ttp80) REVERT: L 30 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8458 (p) REVERT: L 37 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8587 (ptp90) REVERT: L 44 MET cc_start: 0.9481 (mmt) cc_final: 0.9190 (mmt) REVERT: M 123 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: M 247 MET cc_start: 0.8990 (tpp) cc_final: 0.8655 (tmm) REVERT: M 270 MET cc_start: 0.4839 (mpt) cc_final: 0.4252 (mpt) REVERT: M 357 MET cc_start: 0.3347 (mpp) cc_final: 0.2714 (ttm) REVERT: N 115 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: O 31 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9263 (p) REVERT: O 531 MET cc_start: 0.7875 (ttt) cc_final: 0.7620 (tpt) REVERT: P 203 MET cc_start: 0.9086 (tpt) cc_final: 0.8451 (tpp) REVERT: P 207 ASN cc_start: 0.9028 (m110) cc_final: 0.8283 (m110) REVERT: P 268 LYS cc_start: 0.9255 (mttt) cc_final: 0.8757 (mppt) REVERT: Q 37 LEU cc_start: 0.8292 (mp) cc_final: 0.8076 (mt) REVERT: Q 70 ARG cc_start: 0.8964 (mtm110) cc_final: 0.8409 (ptp90) REVERT: Q 92 MET cc_start: 0.7928 (mtt) cc_final: 0.7495 (ppp) REVERT: Q 96 LYS cc_start: 0.6967 (tptt) cc_final: 0.6277 (tppp) REVERT: Q 110 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8643 (mmm) outliers start: 74 outliers final: 34 residues processed: 327 average time/residue: 0.7740 time to fit residues: 309.2179 Evaluate side-chains 299 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 791 MET Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 110 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 250 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 427 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 426 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.077995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047539 restraints weight = 132764.126| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.87 r_work: 0.2712 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43523 Z= 0.198 Angle : 0.601 13.030 58957 Z= 0.300 Chirality : 0.043 0.223 6621 Planarity : 0.004 0.055 7442 Dihedral : 9.773 156.477 6194 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 1.34 % Allowed : 11.79 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 5193 helix: 1.07 (0.12), residues: 1906 sheet: -0.00 (0.19), residues: 695 loop : -0.51 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 70 TYR 0.037 0.001 TYR Q 87 PHE 0.017 0.001 PHE B 934 TRP 0.034 0.001 TRP N 123 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00469 (43497) covalent geometry : angle 0.59298 (58921) hydrogen bonds : bond 0.03803 ( 1679) hydrogen bonds : angle 4.38917 ( 4749) metal coordination : bond 0.00932 ( 26) metal coordination : angle 3.96300 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 1.625 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: B 427 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8975 (mmmt) REVERT: B 431 MET cc_start: 0.8676 (ttt) cc_final: 0.8265 (ttm) REVERT: D 5 ASP cc_start: 0.8064 (t0) cc_final: 0.7341 (t0) REVERT: D 18 GLN cc_start: 0.8987 (tt0) cc_final: 0.8756 (pt0) REVERT: D 26 GLN cc_start: 0.9301 (pp30) cc_final: 0.9020 (pp30) REVERT: E 152 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7838 (p) REVERT: G 120 PHE cc_start: 0.7045 (m-80) cc_final: 0.6597 (p90) REVERT: G 148 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6695 (pt) REVERT: I 91 MET cc_start: 0.5809 (mtp) cc_final: 0.5133 (mmm) REVERT: K 124 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8091 (tm-30) REVERT: K 128 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7812 (ttp80) REVERT: L 30 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8428 (p) REVERT: L 37 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8735 (ptp90) REVERT: L 44 MET cc_start: 0.9488 (mmt) cc_final: 0.9194 (mmt) REVERT: M 123 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: M 247 MET cc_start: 0.8991 (tpp) cc_final: 0.8675 (tmm) REVERT: M 270 MET cc_start: 0.4858 (mpt) cc_final: 0.4230 (mpt) REVERT: M 357 MET cc_start: 0.3248 (mpp) cc_final: 0.2677 (ttm) REVERT: N 115 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: O 118 MET cc_start: 0.9261 (ttm) cc_final: 0.8955 (mtm) REVERT: O 531 MET cc_start: 0.7913 (ttt) cc_final: 0.7649 (tpt) REVERT: P 186 LYS cc_start: 0.9331 (mttm) cc_final: 0.9027 (tppt) REVERT: P 203 MET cc_start: 0.9071 (tpt) cc_final: 0.8717 (tpp) REVERT: P 207 ASN cc_start: 0.9042 (m110) cc_final: 0.8666 (m110) REVERT: P 268 LYS cc_start: 0.9257 (mttt) cc_final: 0.8786 (mppt) REVERT: Q 37 LEU cc_start: 0.8334 (mp) cc_final: 0.8123 (mt) REVERT: Q 49 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8320 (mmpt) REVERT: Q 92 MET cc_start: 0.7947 (mtt) cc_final: 0.7497 (ppp) REVERT: Q 96 LYS cc_start: 0.6996 (tptt) cc_final: 0.6347 (tppp) REVERT: Q 110 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8248 (mmm) outliers start: 62 outliers final: 35 residues processed: 315 average time/residue: 0.8022 time to fit residues: 305.4591 Evaluate side-chains 303 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 88 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 497 optimal weight: 30.0000 chunk 501 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 493 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1286 HIS ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN E 148 HIS K 81 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.077613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046723 restraints weight = 135508.693| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.91 r_work: 0.2690 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 43523 Z= 0.233 Angle : 0.631 14.224 58957 Z= 0.314 Chirality : 0.044 0.269 6621 Planarity : 0.004 0.060 7442 Dihedral : 9.786 155.955 6194 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 1.30 % Allowed : 12.18 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5193 helix: 1.07 (0.12), residues: 1914 sheet: -0.14 (0.19), residues: 710 loop : -0.54 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q 70 TYR 0.040 0.001 TYR Q 87 PHE 0.021 0.001 PHE B 934 TRP 0.044 0.001 TRP N 123 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00554 (43497) covalent geometry : angle 0.62265 (58921) hydrogen bonds : bond 0.03932 ( 1679) hydrogen bonds : angle 4.44018 ( 4749) metal coordination : bond 0.01077 ( 26) metal coordination : angle 4.12972 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 258 time to evaluate : 1.638 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: A 332 MET cc_start: 0.7582 (mmm) cc_final: 0.7377 (mmp) REVERT: B 427 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8972 (mmmt) REVERT: B 431 MET cc_start: 0.8707 (ttt) cc_final: 0.8247 (ttm) REVERT: B 452 MET cc_start: 0.9512 (tpp) cc_final: 0.9294 (mmm) REVERT: D 5 ASP cc_start: 0.8207 (t0) cc_final: 0.7486 (t0) REVERT: D 18 GLN cc_start: 0.8988 (tt0) cc_final: 0.8760 (pt0) REVERT: D 26 GLN cc_start: 0.9301 (pp30) cc_final: 0.9049 (pp30) REVERT: D 112 GLN cc_start: 0.8565 (pt0) cc_final: 0.8327 (pm20) REVERT: E 54 ARG cc_start: 0.8376 (pmt170) cc_final: 0.8013 (pmt-80) REVERT: E 152 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7810 (p) REVERT: G 120 PHE cc_start: 0.7157 (m-80) cc_final: 0.6759 (p90) REVERT: G 148 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6789 (pt) REVERT: I 80 MET cc_start: 0.7023 (tpp) cc_final: 0.6552 (mtt) REVERT: I 91 MET cc_start: 0.5843 (mtp) cc_final: 0.5141 (mmm) REVERT: K 128 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7766 (ttp80) REVERT: L 37 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8736 (ptp90) REVERT: L 44 MET cc_start: 0.9493 (mmt) cc_final: 0.9233 (mmt) REVERT: M 123 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: M 247 MET cc_start: 0.8986 (tpp) cc_final: 0.8663 (tmm) REVERT: M 270 MET cc_start: 0.4717 (mpt) cc_final: 0.4134 (mpt) REVERT: M 357 MET cc_start: 0.3235 (mpp) cc_final: 0.2674 (ttm) REVERT: N 115 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: O 31 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9273 (p) REVERT: O 118 MET cc_start: 0.9274 (ttm) cc_final: 0.8941 (mtm) REVERT: O 531 MET cc_start: 0.7895 (ttt) cc_final: 0.7647 (tpt) REVERT: P 186 LYS cc_start: 0.9336 (mttm) cc_final: 0.9024 (tppt) REVERT: P 203 MET cc_start: 0.9102 (tpt) cc_final: 0.8738 (tpp) REVERT: P 207 ASN cc_start: 0.9062 (m110) cc_final: 0.8612 (m110) REVERT: P 210 PHE cc_start: 0.8595 (m-80) cc_final: 0.8333 (m-80) REVERT: P 268 LYS cc_start: 0.9271 (mttt) cc_final: 0.8839 (mppt) REVERT: Q 37 LEU cc_start: 0.8375 (mp) cc_final: 0.8173 (mt) REVERT: Q 49 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8358 (mmpt) REVERT: Q 92 MET cc_start: 0.7992 (mtt) cc_final: 0.7523 (ppp) REVERT: Q 110 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8464 (mmm) outliers start: 60 outliers final: 35 residues processed: 308 average time/residue: 0.7793 time to fit residues: 292.2931 Evaluate side-chains 297 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 480 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 458 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 418 optimal weight: 40.0000 chunk 243 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 486 optimal weight: 30.0000 chunk 414 optimal weight: 40.0000 chunk 502 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.076687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.045712 restraints weight = 135428.579| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.92 r_work: 0.2660 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 43523 Z= 0.319 Angle : 0.703 15.406 58957 Z= 0.350 Chirality : 0.047 0.311 6621 Planarity : 0.005 0.060 7442 Dihedral : 9.901 154.840 6194 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 1.34 % Allowed : 12.12 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 5193 helix: 0.95 (0.12), residues: 1913 sheet: -0.25 (0.19), residues: 701 loop : -0.64 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 369 TYR 0.029 0.002 TYR B 357 PHE 0.026 0.002 PHE I 4 TRP 0.047 0.002 TRP N 123 HIS 0.015 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00754 (43497) covalent geometry : angle 0.69315 (58921) hydrogen bonds : bond 0.04445 ( 1679) hydrogen bonds : angle 4.62294 ( 4749) metal coordination : bond 0.01458 ( 26) metal coordination : angle 4.73685 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8956 (mmmt) REVERT: B 452 MET cc_start: 0.9502 (tpp) cc_final: 0.9261 (mmm) REVERT: B 929 MET cc_start: 0.8829 (ttm) cc_final: 0.8557 (ttt) REVERT: B 1053 ASP cc_start: 0.8693 (m-30) cc_final: 0.8316 (m-30) REVERT: D 5 ASP cc_start: 0.8178 (t0) cc_final: 0.7528 (t0) REVERT: D 18 GLN cc_start: 0.8991 (tt0) cc_final: 0.8749 (pt0) REVERT: D 26 GLN cc_start: 0.9325 (pp30) cc_final: 0.9085 (pp30) REVERT: D 112 GLN cc_start: 0.8562 (pt0) cc_final: 0.8333 (pm20) REVERT: E 152 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7900 (p) REVERT: G 120 PHE cc_start: 0.7355 (m-80) cc_final: 0.6903 (p90) REVERT: G 148 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6570 (pt) REVERT: I 80 MET cc_start: 0.6937 (tpp) cc_final: 0.6480 (mtt) REVERT: I 91 MET cc_start: 0.5949 (mtp) cc_final: 0.5009 (tpp) REVERT: K 128 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7717 (ttp80) REVERT: L 37 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8716 (ttm170) REVERT: M 123 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: M 247 MET cc_start: 0.8974 (tpp) cc_final: 0.8650 (tmm) REVERT: M 270 MET cc_start: 0.4972 (mpt) cc_final: 0.4370 (mpt) REVERT: M 357 MET cc_start: 0.3432 (mpp) cc_final: 0.2885 (ttm) REVERT: N 115 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: O 31 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9233 (p) REVERT: O 118 MET cc_start: 0.9284 (ttm) cc_final: 0.8957 (mtm) REVERT: O 531 MET cc_start: 0.7817 (ttt) cc_final: 0.7523 (tpt) REVERT: P 186 LYS cc_start: 0.9328 (mttm) cc_final: 0.9019 (tppt) REVERT: P 203 MET cc_start: 0.9151 (tpt) cc_final: 0.8589 (tpp) REVERT: P 207 ASN cc_start: 0.9062 (m110) cc_final: 0.8270 (m110) REVERT: P 210 PHE cc_start: 0.8559 (m-80) cc_final: 0.8295 (m-80) REVERT: P 266 HIS cc_start: 0.8935 (m90) cc_final: 0.8562 (m-70) REVERT: P 268 LYS cc_start: 0.9265 (mttt) cc_final: 0.8852 (mppt) REVERT: Q 92 MET cc_start: 0.8118 (mtt) cc_final: 0.7678 (ppp) REVERT: Q 108 ARG cc_start: 0.8947 (ptm160) cc_final: 0.8524 (pmm-80) outliers start: 62 outliers final: 37 residues processed: 306 average time/residue: 0.7861 time to fit residues: 293.3532 Evaluate side-chains 295 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain Q residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 126 optimal weight: 0.7980 chunk 367 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 516 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 366 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 415 optimal weight: 50.0000 chunk 429 optimal weight: 6.9990 chunk 473 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 677 HIS ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN E 98 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.078421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048229 restraints weight = 132559.765| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.86 r_work: 0.2734 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43523 Z= 0.118 Angle : 0.604 14.500 58957 Z= 0.300 Chirality : 0.042 0.287 6621 Planarity : 0.004 0.054 7442 Dihedral : 9.741 155.245 6194 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 0.80 % Allowed : 12.85 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.12), residues: 5193 helix: 1.18 (0.12), residues: 1896 sheet: -0.16 (0.19), residues: 703 loop : -0.48 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG Q 70 TYR 0.033 0.001 TYR Q 87 PHE 0.019 0.001 PHE A 462 TRP 0.042 0.001 TRP N 123 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00266 (43497) covalent geometry : angle 0.59695 (58921) hydrogen bonds : bond 0.03449 ( 1679) hydrogen bonds : angle 4.32348 ( 4749) metal coordination : bond 0.00518 ( 26) metal coordination : angle 3.75156 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10386 Ramachandran restraints generated. 5193 Oldfield, 0 Emsley, 5193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.672 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 332 MET cc_start: 0.7493 (mmp) cc_final: 0.7245 (mmp) REVERT: A 1185 MET cc_start: 0.8595 (ptt) cc_final: 0.8365 (pmm) REVERT: B 427 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8952 (mmmt) REVERT: B 929 MET cc_start: 0.8840 (ttm) cc_final: 0.8558 (ttt) REVERT: D 5 ASP cc_start: 0.8139 (t0) cc_final: 0.7443 (t0) REVERT: D 18 GLN cc_start: 0.9001 (tt0) cc_final: 0.8717 (pt0) REVERT: D 26 GLN cc_start: 0.9303 (pp30) cc_final: 0.9045 (pp30) REVERT: D 112 GLN cc_start: 0.8583 (pt0) cc_final: 0.8330 (pm20) REVERT: E 152 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7890 (p) REVERT: I 91 MET cc_start: 0.6130 (mtp) cc_final: 0.5104 (tpp) REVERT: L 25 GLU cc_start: 0.9076 (mp0) cc_final: 0.8707 (mp0) REVERT: L 37 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8557 (ptp90) REVERT: L 44 MET cc_start: 0.9431 (mmt) cc_final: 0.9159 (mmt) REVERT: M 123 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6836 (pm20) REVERT: M 247 MET cc_start: 0.8986 (tpp) cc_final: 0.8655 (tmm) REVERT: M 270 MET cc_start: 0.4996 (mpt) cc_final: 0.4387 (mpt) REVERT: M 357 MET cc_start: 0.3410 (mpp) cc_final: 0.2896 (ttm) REVERT: N 115 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: O 31 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9275 (p) REVERT: O 118 MET cc_start: 0.9270 (ttm) cc_final: 0.8959 (mtm) REVERT: O 133 MET cc_start: 0.5051 (ptt) cc_final: 0.4420 (pmt) REVERT: O 531 MET cc_start: 0.7993 (ttt) cc_final: 0.7764 (tpt) REVERT: P 186 LYS cc_start: 0.9313 (mttm) cc_final: 0.8998 (tppt) REVERT: P 203 MET cc_start: 0.9124 (tpt) cc_final: 0.8798 (tpp) REVERT: P 207 ASN cc_start: 0.9073 (m110) cc_final: 0.8645 (m110) REVERT: P 210 PHE cc_start: 0.8595 (m-80) cc_final: 0.8329 (m-80) REVERT: P 268 LYS cc_start: 0.9273 (mttt) cc_final: 0.8865 (mppt) REVERT: Q 49 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8369 (mmpt) REVERT: Q 92 MET cc_start: 0.8163 (mtt) cc_final: 0.7631 (ppp) REVERT: Q 108 ARG cc_start: 0.9225 (ptm160) cc_final: 0.8571 (pmm-80) REVERT: Q 110 MET cc_start: 0.8673 (mtp) cc_final: 0.8204 (mmm) outliers start: 37 outliers final: 21 residues processed: 290 average time/residue: 0.8200 time to fit residues: 286.0224 Evaluate side-chains 279 residues out of total 4630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 59 TRP Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain Q residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 54 optimal weight: 3.9990 chunk 487 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 chunk 383 optimal weight: 7.9990 chunk 400 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 43 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.076872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.046708 restraints weight = 134671.004| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.67 r_work: 0.2677 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 43523 Z= 0.282 Angle : 0.677 14.537 58957 Z= 0.336 Chirality : 0.045 0.363 6621 Planarity : 0.004 0.055 7442 Dihedral : 9.793 154.497 6194 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer: Outliers : 0.84 % Allowed : 12.89 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 5193 helix: 1.11 (0.12), residues: 1912 sheet: -0.26 (0.19), residues: 701 loop : -0.59 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 70 TYR 0.027 0.002 TYR Q 87 PHE 0.022 0.002 PHE I 4 TRP 0.053 0.002 TRP N 123 HIS 0.014 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00666 (43497) covalent geometry : angle 0.66860 (58921) hydrogen bonds : bond 0.04070 ( 1679) hydrogen bonds : angle 4.47922 ( 4749) metal coordination : bond 0.01250 ( 26) metal coordination : angle 4.43015 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16324.58 seconds wall clock time: 277 minutes 52.32 seconds (16672.32 seconds total)