Starting phenix.real_space_refine on Sat Mar 7 11:46:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ae3_11738/03_2026/7ae3_11738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ae3_11738/03_2026/7ae3_11738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ae3_11738/03_2026/7ae3_11738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ae3_11738/03_2026/7ae3_11738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ae3_11738/03_2026/7ae3_11738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ae3_11738/03_2026/7ae3_11738.map" } resolution = 3.1 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 26757 2.51 5 N 7380 2.21 5 O 8046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42525 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 10765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1370, 10765 Classifications: {'peptide': 1370} Link IDs: {'PTRANS': 65, 'TRANS': 1304} Chain breaks: 2 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 69 100.390 68.265 120.892 1.00123.46 S ATOM 565 SG CYS A 72 98.286 64.284 120.898 1.00119.00 S ATOM 613 SG CYS A 79 96.753 67.087 119.058 1.00114.39 S ATOM 854 SG CYS A 109 68.039 95.745 145.709 1.00134.61 S ATOM 876 SG CYS A 112 68.208 92.652 148.185 1.00137.99 S ATOM 1245 SG CYS A 156 64.286 93.750 147.420 1.00147.45 S ATOM 1271 SG CYS A 159 67.020 95.855 149.251 1.00148.32 S ATOM 19032 SG CYS B1080 84.051 62.012 130.311 1.00112.41 S ATOM 19051 SG CYS B1083 83.773 65.669 130.511 1.00110.35 S ATOM 19117 SG CYS B1092 87.128 64.186 130.276 1.00113.94 S ATOM 19145 SG CYS B1095 84.940 64.186 133.985 1.00115.16 S ATOM 28260 SG CYS I 5 56.575 148.198 110.415 1.00114.52 S ATOM 28277 SG CYS I 8 60.056 146.253 111.693 1.00114.88 S ATOM 28408 SG CYS I 25 57.316 144.935 113.573 1.00122.98 S ATOM 28429 SG CYS I 28 57.666 148.620 113.767 1.00124.29 S ATOM 29123 SG CYS J 7 88.990 75.449 49.431 1.00 69.10 S ATOM 29147 SG CYS J 10 88.217 72.441 46.598 1.00 67.05 S ATOM 29411 SG CYS J 44 85.751 75.258 47.181 1.00 75.17 S ATOM 29417 SG CYS J 45 89.196 75.520 45.132 1.00 73.81 S ATOM 30506 SG CYS L 19 122.273 91.738 71.855 1.00 96.02 S ATOM 30525 SG CYS L 22 124.259 92.470 68.953 1.00104.23 S ATOM 30642 SG CYS L 36 125.830 92.379 72.354 1.00107.96 S Time building chain proxies: 8.86, per 1000 atoms: 0.21 Number of scatterers: 42525 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 8046 8.00 N 7380 7.00 C 26757 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: 3.85 Conformation dependent library (CDL) restraints added in 2.0 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="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 296 " 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 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " 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 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9850 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 57 sheets defined 39.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.579A pdb=" N GLY A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.674A pdb=" N LYS A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 removed outlier: 3.534A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.821A pdb=" N PHE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.788A pdb=" N HIS A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.891A 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 222 through 228 Processing helix chain 'A' and resid 229 through 230 No H-bonds generated for 'chain 'A' and resid 229 through 230' Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.540A pdb=" N VAL A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Proline residue: A 236 - end of helix 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 297 removed outlier: 3.514A pdb=" N GLU A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.578A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.616A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.665A 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: 3.975A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 522 removed outlier: 3.588A pdb=" N LEU A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) 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 577 removed outlier: 4.020A pdb=" N ASP A 576 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 4.184A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.779A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 695 removed outlier: 3.880A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.751A 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: 3.630A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 768 removed outlier: 3.580A pdb=" N LEU A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 760 " --> pdb=" O LEU A 756 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.740A pdb=" N ILE A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.658A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N MET A 871 " --> pdb=" O GLU A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.865A 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 954 through 955 No H-bonds generated for 'chain 'A' and resid 954 through 955' Processing helix chain 'A' and resid 956 through 961 removed outlier: 3.983A pdb=" N CYS A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 987 removed outlier: 3.610A pdb=" N LEU A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 removed outlier: 3.595A pdb=" N LEU A1003 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1024 Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1044 through 1047 Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.635A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1104 removed outlier: 3.754A pdb=" N ALA A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A1100 " --> pdb=" O ASP A1096 " (cutoff:3.500A) removed outlier: 3.703A 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 Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 3.557A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1238 removed outlier: 3.536A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A1238 " --> pdb=" O ALA A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1246 removed outlier: 3.978A pdb=" N THR A1246 " --> pdb=" O GLY A1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1243 through 1246' Processing helix chain 'A' and resid 1250 through 1259 removed outlier: 3.504A pdb=" N VAL A1254 " --> pdb=" O ASN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1278 removed outlier: 3.623A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 4.051A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 removed outlier: 3.777A pdb=" N LYS A1310 " --> pdb=" O PHE A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1320 Processing helix chain 'A' and resid 1323 through 1334 removed outlier: 3.694A pdb=" N HIS A1327 " --> pdb=" O LYS A1323 " (cutoff:3.500A) removed outlier: 4.031A 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: 3.634A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.884A 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: 3.914A pdb=" N PHE A1384 " --> pdb=" O THR A1381 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS A1385 " --> pdb=" O ASN A1382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1381 through 1385' Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.795A pdb=" N LYS B 26 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 27' Processing helix chain 'B' and resid 28 through 34 Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.645A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.550A pdb=" N ILE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 273 Proline residue: B 267 - end of helix removed outlier: 3.507A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 3.567A pdb=" N ASN B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.767A pdb=" N LEU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.946A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.546A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.683A pdb=" N LYS B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 444 through 452 removed outlier: 3.845A pdb=" N ALA B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.543A pdb=" N GLN B 475 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.959A pdb=" N LYS B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.944A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.791A 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: 3.525A pdb=" N GLU B 627 " --> pdb=" O ASP B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.508A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.618A pdb=" N LEU B 671 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.884A pdb=" N ASN B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'B' and resid 722 through 728 removed outlier: 3.571A pdb=" N GLU B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.564A pdb=" N LYS B 732 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.712A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 954 removed outlier: 3.863A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.644A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 977 " --> pdb=" O CYS B 973 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 979 " --> pdb=" O ASP B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1019 Processing helix chain 'B' and resid 1038 through 1042 removed outlier: 3.501A pdb=" N ASP B1042 " --> pdb=" O ARG B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1058 removed outlier: 3.625A pdb=" N ASP B1053 " --> pdb=" O GLU B1049 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B1055 " --> pdb=" O GLU B1051 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B1057 " --> pdb=" O ASP B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1069 removed outlier: 3.688A pdb=" N LEU B1068 " --> pdb=" O LEU B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1117 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: 4.183A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.704A pdb=" N LEU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.518A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.526A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.545A pdb=" N ASP C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.528A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 27 removed outlier: 3.810A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.647A pdb=" N ILE D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 73 removed outlier: 3.569A pdb=" N VAL D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 77 removed outlier: 4.296A pdb=" N LYS D 77 " --> pdb=" O LYS D 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 74 through 77' Processing helix chain 'D' and resid 79 through 89 removed outlier: 3.559A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS D 89 " --> pdb=" O GLN D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 124 removed outlier: 3.503A pdb=" N LEU D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 removed outlier: 3.722A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.723A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.903A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.617A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.024A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.874A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.775A pdb=" N GLN E 169 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.542A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.568A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) 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 removed outlier: 3.730A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.771A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 removed outlier: 3.610A pdb=" N LEU G 114 " --> pdb=" O PRO G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.906A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.720A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.940A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.753A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 128 removed outlier: 3.893A pdb=" N PHE K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG K 128 " --> pdb=" O GLN K 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.617A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 154 removed outlier: 3.895A pdb=" N ASP M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 201 Processing helix chain 'M' and resid 215 through 221 removed outlier: 3.606A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 226 Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 277 through 289 Processing helix chain 'M' and resid 294 through 302 removed outlier: 4.278A pdb=" N MET M 298 " --> pdb=" O PHE M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 315 Processing helix chain 'M' and resid 328 through 333 removed outlier: 4.122A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 363 removed outlier: 4.404A pdb=" N VAL M 356 " --> pdb=" O GLY M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 375 removed outlier: 3.750A pdb=" N VAL M 374 " --> pdb=" O GLU M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 386 removed outlier: 3.996A pdb=" N ASP M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 410 removed outlier: 4.158A pdb=" N ILE M 409 " --> pdb=" O GLY M 406 " (cutoff:3.500A) removed outlier: 4.263A 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: 4.302A pdb=" N HIS M 420 " --> pdb=" O VAL M 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 124 removed outlier: 3.810A 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 259 removed outlier: 3.540A pdb=" N GLU N 257 " --> pdb=" O GLU N 253 " (cutoff:3.500A) 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: 3.559A pdb=" N HIS N 395 " --> pdb=" O SER N 391 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 18 removed outlier: 3.662A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 32 removed outlier: 3.604A pdb=" N HIS O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY O 32 " --> pdb=" O LEU O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 44 removed outlier: 3.856A pdb=" N ALA O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 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 removed outlier: 3.530A pdb=" N VAL O 82 " --> pdb=" O GLN O 78 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 78 through 84' Processing helix chain 'O' and resid 87 through 98 removed outlier: 3.548A pdb=" N LYS O 96 " --> pdb=" O ILE O 92 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 Processing helix chain 'O' and resid 118 through 129 removed outlier: 3.624A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA O 126 " --> pdb=" O VAL O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 3.682A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG O 150 " --> pdb=" O ASN O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 removed outlier: 3.797A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE O 251 " --> pdb=" O ARG O 247 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN O 257 " --> pdb=" O SER O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 274 removed outlier: 3.589A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 removed outlier: 3.688A pdb=" N PHE O 294 " --> pdb=" O SER O 290 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG O 295 " --> pdb=" O ASN O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 315 Processing helix chain 'O' and resid 338 through 359 removed outlier: 3.919A pdb=" N VAL O 353 " --> pdb=" O THR O 349 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL O 354 " --> pdb=" O LEU O 350 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN O 355 " --> pdb=" O GLU O 351 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU O 356 " --> pdb=" O SER O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 372 removed outlier: 4.031A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU O 370 " --> pdb=" O PHE O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 384 Processing helix chain 'O' and resid 390 through 400 removed outlier: 3.628A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET O 398 " --> pdb=" O MET O 394 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU O 399 " --> pdb=" O LEU O 395 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER O 400 " --> pdb=" O TYR O 396 " (cutoff:3.500A) 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 457 removed outlier: 3.794A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN O 457 " --> pdb=" O GLU O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 removed outlier: 3.625A pdb=" N GLU O 462 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.881A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU O 484 " --> pdb=" O GLU O 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 480 through 484' Processing helix chain 'O' and resid 495 through 530 removed outlier: 3.687A pdb=" N LYS O 508 " --> pdb=" O ARG O 504 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 197 removed outlier: 3.649A pdb=" N GLU P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS P 186 " --> pdb=" O GLN P 182 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS P 191 " --> pdb=" O PHE P 187 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA P 192 " --> pdb=" O LEU P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 removed outlier: 3.516A pdb=" N ASN P 207 " --> pdb=" O MET P 203 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 224 removed outlier: 3.509A pdb=" N ILE P 220 " --> pdb=" O VAL P 216 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS P 221 " --> pdb=" O TRP P 217 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU P 222 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY P 224 " --> pdb=" O ILE P 220 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 245 removed outlier: 4.063A pdb=" N THR P 237 " --> pdb=" O GLU P 233 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN P 240 " --> pdb=" O GLU P 236 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR P 241 " --> pdb=" O THR P 237 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU P 242 " --> pdb=" O ILE P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.655A pdb=" N GLY P 288 " --> pdb=" O ALA P 285 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS P 290 " --> pdb=" O CYS P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 296 removed outlier: 3.568A 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 removed outlier: 3.600A pdb=" N THR P 311 " --> pdb=" O CYS P 307 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP P 313 " --> pdb=" O TYR P 309 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 20 removed outlier: 3.594A pdb=" N VAL Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 69 removed outlier: 3.632A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU Q 66 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.711A pdb=" N ARG Q 90 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.682A pdb=" N MET Q 111 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.713A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL G 75 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 2 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.601A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL G 75 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA G 57 " --> pdb=" O HIS A1364 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A1362 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 7.112A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.519A 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: 6.914A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 84 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.609A 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: 3.505A pdb=" N LYS A 167 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.012A 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 360 Processing sheet with id=AA7, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 3.564A pdb=" N SER A 364 " --> pdb=" O ARG B1023 " (cutoff:3.500A) removed outlier: 3.925A 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: 6.879A pdb=" N ILE A 449 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 421 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU A 451 " --> pdb=" O ASN A 419 " (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: 6.429A 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: 6.866A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1241 through 1242 removed outlier: 4.410A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LEU I 53 " --> pdb=" O ALA A1210 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE A1212 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 7.346A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1165 through 1166 removed outlier: 3.941A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 66 removed outlier: 5.709A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 117 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA B 130 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYR B 119 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG B 128 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.736A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.414A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.531A pdb=" N THR B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 212 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 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 544 through 549 removed outlier: 6.545A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE B 537 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.958A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.958A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 720 through 721 removed outlier: 3.619A pdb=" N LYS B 721 " --> pdb=" O HIS B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 927 through 929 removed outlier: 8.384A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 755 through 758 removed outlier: 5.378A pdb=" N LEU B 755 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 909 " --> pdb=" O LEU B 755 " (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 795 through 796 removed outlier: 3.787A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 826 through 828 removed outlier: 6.758A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 3.809A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 57 removed outlier: 5.917A pdb=" N VAL C 51 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL C 66 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL C 53 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP C 64 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 60 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 57 removed outlier: 5.917A pdb=" N VAL C 51 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL C 66 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL C 53 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP C 64 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 60 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.724A pdb=" N LEU C 142 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.679A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 164 " --> pdb=" O THR C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.740A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.716A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE4, first strand: chain 'E' and resid 62 through 63 removed outlier: 5.967A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ARG E 101 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.011A 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=AE5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.723A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.938A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 196 through 197 removed outlier: 5.503A pdb=" N VAL G 152 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER G 189 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N TYR G 184 " --> pdb=" O PHE G 104 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP G 106 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU G 186 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP G 106 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL G 99 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU G 108 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 9 removed outlier: 6.770A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (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: 3.558A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP I 106 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.989A 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 Processing sheet with id=AF4, first strand: chain 'N' and resid 370 through 387 removed outlier: 3.531A pdb=" N GLY N 371 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS M 55 " --> pdb=" O LYS M 50 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL M 56 " --> pdb=" O SER M 104 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU N 357 " --> pdb=" O TYR M 30 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE N 356 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS N 380 " --> pdb=" O PHE N 356 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU N 266 " --> pdb=" O VAL N 379 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS N 381 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 5.245A 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: 3.578A 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 removed outlier: 3.561A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) 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 1533 hydrogen bonds defined for protein. 4293 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: 11.82 Time building geometry restraints manager: 5.26 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: 17702 1.43 - 1.64: 25250 1.64 - 1.85: 446 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 43410 Sorted by residual: bond pdb=" CA TYR A1187 " pdb=" C TYR A1187 " ideal model delta sigma weight residual 1.523 1.619 -0.096 1.34e-02 5.57e+03 5.13e+01 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.337 1.391 -0.055 1.06e-02 8.90e+03 2.65e+01 bond pdb=" C LYS D 55 " pdb=" N THR D 56 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.48e-02 4.57e+03 7.71e+00 bond pdb=" C GLN G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.11e-02 8.12e+03 7.54e+00 bond pdb=" C GLN B 716 " pdb=" N LYS B 717 " ideal model delta sigma weight residual 1.329 1.283 0.046 1.86e-02 2.89e+03 6.03e+00 ... (remaining 43405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 57851 3.03 - 6.07: 855 6.07 - 9.10: 81 9.10 - 12.13: 13 12.13 - 15.16: 2 Bond angle restraints: 58802 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 121.97 137.13 -15.16 1.80e+00 3.09e-01 7.10e+01 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 120.01 -10.67 2.08e+00 2.31e-01 2.63e+01 angle pdb=" N ILE A1153 " pdb=" CA ILE A1153 " pdb=" C ILE A1153 " ideal model delta sigma weight residual 110.05 104.60 5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" C ASN B 52 " pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta sigma weight residual 122.77 117.70 5.07 1.05e+00 9.07e-01 2.34e+01 angle pdb=" C ILE A1153 " pdb=" N CYS A1154 " pdb=" CA CYS A1154 " ideal model delta sigma weight residual 122.74 129.52 -6.78 1.44e+00 4.82e-01 2.21e+01 ... (remaining 58797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.35: 26098 30.35 - 60.69: 456 60.69 - 91.04: 36 91.04 - 121.38: 0 121.38 - 151.73: 2 Dihedral angle restraints: 26592 sinusoidal: 11359 harmonic: 15233 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 -128.50 -51.50 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA ARG A 464 " pdb=" C ARG A 464 " pdb=" N GLN A 465 " pdb=" CA GLN A 465 " ideal model delta harmonic sigma weight residual 180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ARG E 52 " pdb=" C ARG E 52 " pdb=" N PRO E 53 " pdb=" CA PRO E 53 " ideal model delta harmonic sigma weight residual 180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 26589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5533 0.075 - 0.150: 985 0.150 - 0.225: 77 0.225 - 0.301: 11 0.301 - 0.376: 2 Chirality restraints: 6608 Sorted by residual: chirality pdb=" CA ALA G 137 " pdb=" N ALA G 137 " pdb=" C ALA G 137 " pdb=" CB ALA G 137 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.53e+00 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 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C3' A R 14 " pdb=" C4' A R 14 " pdb=" O3' A R 14 " pdb=" C2' A R 14 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 6605 not shown) Planarity restraints: 7427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN M 281 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLN M 281 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN M 281 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE M 282 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1003 " -0.027 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR B1003 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B1003 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B1003 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B1003 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B1003 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B1003 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1003 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 467 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO B 468 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " 0.041 5.00e-02 4.00e+02 ... (remaining 7424 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 19 2.33 - 2.97: 18305 2.97 - 3.62: 59598 3.62 - 4.26: 95685 4.26 - 4.90: 158318 Nonbonded interactions: 331925 Sorted by model distance: nonbonded pdb=" O3' G R 19 " pdb="MG MG R 101 " model vdw 1.688 2.170 nonbonded pdb=" OD1 ASP A 501 " pdb="MG MG R 101 " model vdw 1.851 2.170 nonbonded pdb=" OD2 ASP A 499 " pdb="MG MG R 101 " model vdw 1.980 2.170 nonbonded pdb=" O TYR B 618 " pdb=" OG SER M 269 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG R 101 " model vdw 2.264 2.170 ... (remaining 331920 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: 2.430 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 53.280 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.012 0.843 43436 Z= 0.429 Angle : 1.087 48.621 58838 Z= 0.551 Chirality : 0.057 0.376 6608 Planarity : 0.007 0.075 7427 Dihedral : 11.227 151.727 16742 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 0.37 % Allowed : 2.75 % Favored : 96.88 % Cbeta Deviations : 0.02 % 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: -4.00 (0.09), residues: 5180 helix: -3.46 (0.08), residues: 1758 sheet: -2.02 (0.17), residues: 704 loop : -2.22 (0.10), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG M 351 TYR 0.054 0.003 TYR B1003 PHE 0.034 0.003 PHE M 400 TRP 0.025 0.003 TRP N 123 HIS 0.013 0.003 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00806 (43410) covalent geometry : angle 0.97142 (58802) hydrogen bonds : bond 0.25687 ( 1486) hydrogen bonds : angle 8.53685 ( 4293) metal coordination : bond 0.34283 ( 26) metal coordination : angle 19.72699 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 668 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ILE cc_start: 0.8321 (mt) cc_final: 0.8110 (mm) REVERT: D 5 ASP cc_start: 0.8354 (t0) cc_final: 0.7992 (t0) REVERT: D 17 PHE cc_start: 0.8812 (t80) cc_final: 0.8607 (t80) REVERT: D 18 GLN cc_start: 0.8976 (tt0) cc_final: 0.8613 (pt0) REVERT: D 47 TYR cc_start: 0.8719 (t80) cc_final: 0.8488 (t80) REVERT: D 76 HIS cc_start: 0.7927 (m-70) cc_final: 0.7706 (m-70) REVERT: E 36 THR cc_start: 0.7783 (m) cc_final: 0.7579 (p) REVERT: F 121 ASP cc_start: 0.8017 (p0) cc_final: 0.7791 (m-30) REVERT: G 90 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8409 (mtpt) REVERT: I 39 THR cc_start: 0.4789 (p) cc_final: 0.4421 (m) REVERT: K 119 LYS cc_start: 0.9304 (ttpt) cc_final: 0.9025 (ttpp) REVERT: L 37 ARG cc_start: 0.8204 (tmm160) cc_final: 0.7959 (ptt90) REVERT: M 139 PHE cc_start: 0.7407 (m-80) cc_final: 0.7128 (m-10) REVERT: M 338 SER cc_start: -0.0613 (OUTLIER) cc_final: -0.0909 (p) REVERT: N 375 VAL cc_start: 0.8452 (t) cc_final: 0.8194 (m) REVERT: Q 87 TYR cc_start: 0.7433 (t80) cc_final: 0.6354 (t80) REVERT: Q 91 TYR cc_start: 0.6964 (m-10) cc_final: 0.6632 (m-80) outliers start: 17 outliers final: 3 residues processed: 683 average time/residue: 0.2894 time to fit residues: 316.3290 Evaluate side-chains 345 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 341 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain M residue 341 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 516 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 158 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 355 ASN A 476 HIS A 616 ASN A 662 ASN A 927 ASN A1180 ASN A1202 GLN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 215 ASN B 320 HIS B 346 GLN B 501 HIS B 602 GLN B 677 HIS B 683 ASN B 758 ASN B 901 HIS B 903 GLN B1034 GLN B1100 HIS C 305 HIS D 76 HIS E 148 HIS H 44 ASN H 76 ASN I 10 ASN I 40 ASN I 74 HIS J 61 ASN K 74 HIS K 81 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS M 76 GLN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 ASN N 106 HIS N 111 GLN ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS O 146 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN O 306 GLN O 310 GLN O 339 HIS O 515 GLN P 200 GLN P 201 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.074322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052037 restraints weight = 179794.470| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 5.19 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 43436 Z= 0.192 Angle : 0.692 14.804 58838 Z= 0.357 Chirality : 0.045 0.298 6608 Planarity : 0.006 0.064 7427 Dihedral : 10.183 157.974 6185 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 1.77 % Allowed : 6.82 % Favored : 91.41 % Cbeta Deviations : 0.00 % 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: -2.37 (0.10), residues: 5180 helix: -1.53 (0.11), residues: 1810 sheet: -1.24 (0.18), residues: 721 loop : -1.63 (0.11), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 54 TYR 0.021 0.002 TYR I 30 PHE 0.023 0.002 PHE O 148 TRP 0.022 0.002 TRP N 123 HIS 0.009 0.001 HIS I 21 Details of bonding type rmsd covalent geometry : bond 0.00414 (43410) covalent geometry : angle 0.68110 (58802) hydrogen bonds : bond 0.04256 ( 1486) hydrogen bonds : angle 5.16432 ( 4293) metal coordination : bond 0.01694 ( 26) metal coordination : angle 5.04157 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 362 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8905 (mtp) cc_final: 0.8659 (mtm) REVERT: A 912 MET cc_start: 0.7794 (mmm) cc_final: 0.6976 (mmm) REVERT: A 1048 MET cc_start: 0.8261 (ptt) cc_final: 0.7674 (ptt) REVERT: A 1105 ILE cc_start: 0.8998 (mt) cc_final: 0.8738 (pt) REVERT: A 1167 VAL cc_start: 0.7853 (m) cc_final: 0.7481 (t) REVERT: A 1308 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 1311 MET cc_start: 0.8790 (mtm) cc_final: 0.8039 (mtm) REVERT: B 653 ASP cc_start: 0.7339 (m-30) cc_final: 0.6567 (p0) REVERT: B 1069 MET cc_start: 0.8569 (tpp) cc_final: 0.7961 (tpt) REVERT: C 98 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8729 (p) REVERT: C 212 MET cc_start: 0.8761 (mtt) cc_final: 0.8403 (mtm) REVERT: D 5 ASP cc_start: 0.8541 (t0) cc_final: 0.7976 (t0) REVERT: D 112 GLN cc_start: 0.8939 (mt0) cc_final: 0.8676 (mp10) REVERT: E 36 THR cc_start: 0.8157 (m) cc_final: 0.6111 (p) REVERT: E 55 ARG cc_start: 0.8044 (mpt90) cc_final: 0.7121 (tmm160) REVERT: G 7 MET cc_start: 0.7988 (mtm) cc_final: 0.7476 (ptp) REVERT: G 90 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8384 (mtpt) REVERT: G 142 MET cc_start: 0.8942 (tpp) cc_final: 0.8666 (tpp) REVERT: J 28 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8665 (mm-30) REVERT: K 115 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8550 (mm-30) REVERT: L 27 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7790 (tm-30) REVERT: L 44 MET cc_start: 0.8844 (mmt) cc_final: 0.8238 (mmt) REVERT: M 139 PHE cc_start: 0.7906 (m-80) cc_final: 0.7683 (m-80) REVERT: M 286 MET cc_start: 0.1708 (tpp) cc_final: 0.1472 (tpp) REVERT: M 292 MET cc_start: -0.0833 (ptm) cc_final: -0.1205 (ptp) REVERT: N 116 MET cc_start: 0.8896 (tmm) cc_final: 0.8551 (tmm) REVERT: N 256 ARG cc_start: 0.7802 (ptp-170) cc_final: 0.7468 (ptp-170) REVERT: P 244 TYR cc_start: 0.7723 (m-80) cc_final: 0.7416 (m-80) REVERT: Q 82 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7467 (tm-30) REVERT: Q 91 TYR cc_start: 0.7135 (m-10) cc_final: 0.6839 (m-80) REVERT: Q 104 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8284 (mtm-85) outliers start: 82 outliers final: 42 residues processed: 428 average time/residue: 0.2639 time to fit residues: 186.8780 Evaluate side-chains 343 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 321 LEU Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain P residue 270 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 341 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 426 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 374 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 114 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 374 ASN A 508 HIS A 836 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 HIS B1093 HIS D 60 HIS D 98 GLN I 40 ASN I 61 ASN K 38 HIS ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN M 125 HIS ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 338 GLN N 395 HIS ** O 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.069165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.045762 restraints weight = 178284.001| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 5.25 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 43436 Z= 0.297 Angle : 0.857 41.092 58838 Z= 0.413 Chirality : 0.048 0.298 6608 Planarity : 0.006 0.068 7427 Dihedral : 10.199 155.470 6182 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.29 % Allowed : 8.20 % Favored : 89.51 % Cbeta Deviations : 0.00 % 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: -1.46 (0.11), residues: 5180 helix: -0.54 (0.12), residues: 1843 sheet: -0.97 (0.18), residues: 747 loop : -1.22 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG P 206 TYR 0.054 0.003 TYR O 188 PHE 0.032 0.002 PHE B 326 TRP 0.022 0.002 TRP N 123 HIS 0.016 0.002 HIS O 155 Details of bonding type rmsd covalent geometry : bond 0.00648 (43410) covalent geometry : angle 0.80105 (58802) hydrogen bonds : bond 0.05340 ( 1486) hydrogen bonds : angle 4.96467 ( 4293) metal coordination : bond 0.00818 ( 26) metal coordination : angle 12.35050 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 287 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7930 (t80) REVERT: A 912 MET cc_start: 0.8983 (mmm) cc_final: 0.8644 (mmm) REVERT: A 1048 MET cc_start: 0.7969 (ptt) cc_final: 0.7639 (ptt) REVERT: A 1382 ASN cc_start: 0.8623 (t0) cc_final: 0.8069 (p0) REVERT: B 478 MET cc_start: 0.9238 (mmt) cc_final: 0.8982 (mmt) REVERT: B 719 MET cc_start: 0.9345 (mmm) cc_final: 0.8938 (tpp) REVERT: B 755 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8825 (pp) REVERT: B 1069 MET cc_start: 0.8656 (tpp) cc_final: 0.7636 (tpt) REVERT: C 98 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8751 (p) REVERT: D 5 ASP cc_start: 0.8704 (t0) cc_final: 0.8264 (t0) REVERT: D 18 GLN cc_start: 0.8821 (tt0) cc_final: 0.8378 (tm-30) REVERT: D 22 ASP cc_start: 0.8782 (p0) cc_final: 0.7916 (p0) REVERT: E 94 MET cc_start: 0.7819 (ttt) cc_final: 0.7440 (ttt) REVERT: E 130 PHE cc_start: 0.8281 (m-80) cc_final: 0.7984 (m-80) REVERT: E 152 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8456 (p) REVERT: F 80 MET cc_start: 0.8990 (mmm) cc_final: 0.8727 (mmm) REVERT: G 20 ARG cc_start: 0.8782 (ptm-80) cc_final: 0.8484 (ptm-80) REVERT: G 142 MET cc_start: 0.9059 (tpp) cc_final: 0.8807 (tpp) REVERT: I 1 MET cc_start: 0.5292 (pmm) cc_final: 0.4817 (pmm) REVERT: I 82 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8375 (tp) REVERT: L 27 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7821 (tm-30) REVERT: M 250 MET cc_start: 0.9416 (tpp) cc_final: 0.9198 (mmp) REVERT: M 292 MET cc_start: 0.0111 (ptm) cc_final: -0.0270 (ptp) REVERT: N 116 MET cc_start: 0.9081 (tmm) cc_final: 0.8848 (tmm) REVERT: N 256 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7454 (ptp-170) REVERT: O 474 MET cc_start: 0.0972 (tmm) cc_final: 0.0466 (ptt) REVERT: P 203 MET cc_start: 0.9231 (tpt) cc_final: 0.8834 (mmt) REVERT: P 310 MET cc_start: 0.8670 (tpp) cc_final: 0.8338 (mpp) REVERT: Q 29 ASP cc_start: 0.7692 (m-30) cc_final: 0.7176 (t0) REVERT: Q 111 MET cc_start: 0.8498 (mmm) cc_final: 0.8227 (mmp) outliers start: 106 outliers final: 39 residues processed: 369 average time/residue: 0.2577 time to fit residues: 160.4094 Evaluate side-chains 294 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain Q residue 31 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 130 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 360 optimal weight: 8.9990 chunk 383 optimal weight: 5.9990 chunk 280 optimal weight: 9.9990 chunk 403 optimal weight: 0.0870 chunk 196 optimal weight: 10.0000 chunk 412 optimal weight: 40.0000 chunk 442 optimal weight: 10.0000 chunk 325 optimal weight: 3.9990 chunk 435 optimal weight: 0.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 932 HIS ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS E 148 HIS I 21 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 ASN ** N 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS O 155 HIS O 158 GLN ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.068520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.045328 restraints weight = 177831.569| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.71 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 43436 Z= 0.199 Angle : 0.619 18.356 58838 Z= 0.310 Chirality : 0.044 0.175 6608 Planarity : 0.004 0.057 7427 Dihedral : 9.960 155.799 6180 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 1.73 % Allowed : 9.13 % Favored : 89.14 % Cbeta Deviations : 0.00 % 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: -0.87 (0.11), residues: 5180 helix: 0.16 (0.12), residues: 1840 sheet: -0.87 (0.18), residues: 747 loop : -0.96 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 188 TYR 0.022 0.001 TYR O 188 PHE 0.020 0.001 PHE B 326 TRP 0.016 0.001 TRP P 217 HIS 0.008 0.001 HIS P 297 Details of bonding type rmsd covalent geometry : bond 0.00456 (43410) covalent geometry : angle 0.59830 (58802) hydrogen bonds : bond 0.03558 ( 1486) hydrogen bonds : angle 4.55334 ( 4293) metal coordination : bond 0.01003 ( 26) metal coordination : angle 6.38900 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 265 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8235 (t80) REVERT: A 1048 MET cc_start: 0.7996 (ptt) cc_final: 0.7657 (ptt) REVERT: A 1382 ASN cc_start: 0.8621 (t0) cc_final: 0.8035 (p0) REVERT: B 478 MET cc_start: 0.9256 (mmt) cc_final: 0.9000 (mmt) REVERT: B 719 MET cc_start: 0.9290 (mmm) cc_final: 0.8913 (tpp) REVERT: B 929 MET cc_start: 0.7837 (ttt) cc_final: 0.7384 (ttt) REVERT: B 1069 MET cc_start: 0.8739 (tpp) cc_final: 0.7825 (tpt) REVERT: C 98 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8802 (p) REVERT: C 279 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7604 (ttm-80) REVERT: D 5 ASP cc_start: 0.8762 (t0) cc_final: 0.8284 (t0) REVERT: D 18 GLN cc_start: 0.8723 (tt0) cc_final: 0.8357 (tm-30) REVERT: D 22 ASP cc_start: 0.8684 (p0) cc_final: 0.7642 (p0) REVERT: E 94 MET cc_start: 0.7993 (ttt) cc_final: 0.7727 (ttt) REVERT: E 152 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8500 (p) REVERT: F 80 MET cc_start: 0.8977 (mmm) cc_final: 0.8685 (mmm) REVERT: I 1 MET cc_start: 0.5439 (pmm) cc_final: 0.5089 (pmm) REVERT: I 82 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8388 (tp) REVERT: L 27 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8108 (tm-30) REVERT: L 44 MET cc_start: 0.9096 (mmt) cc_final: 0.8450 (mmt) REVERT: M 292 MET cc_start: -0.1117 (ptm) cc_final: -0.1344 (ptp) REVERT: N 116 MET cc_start: 0.9088 (tmm) cc_final: 0.8860 (tmm) REVERT: N 256 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7406 (ptp-170) REVERT: O 455 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8373 (tppt) REVERT: Q 29 ASP cc_start: 0.7757 (m-30) cc_final: 0.7311 (t0) REVERT: Q 71 MET cc_start: 0.8607 (mtm) cc_final: 0.8381 (mtm) REVERT: Q 82 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7324 (tm-30) REVERT: Q 111 MET cc_start: 0.8899 (mmm) cc_final: 0.8625 (mmp) outliers start: 80 outliers final: 36 residues processed: 323 average time/residue: 0.2332 time to fit residues: 128.9075 Evaluate side-chains 284 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 421 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 464 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 502 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 534 GLN ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 ASN P 297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.067877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044742 restraints weight = 177288.629| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.85 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 43436 Z= 0.182 Angle : 0.619 28.379 58838 Z= 0.300 Chirality : 0.043 0.176 6608 Planarity : 0.004 0.053 7427 Dihedral : 9.848 154.727 6180 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 1.77 % Allowed : 9.65 % Favored : 88.58 % Cbeta Deviations : 0.00 % 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: -0.51 (0.12), residues: 5180 helix: 0.54 (0.13), residues: 1836 sheet: -0.68 (0.19), residues: 741 loop : -0.82 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 90 TYR 0.020 0.001 TYR B 357 PHE 0.020 0.001 PHE B 326 TRP 0.011 0.001 TRP N 123 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00417 (43410) covalent geometry : angle 0.58509 (58802) hydrogen bonds : bond 0.03454 ( 1486) hydrogen bonds : angle 4.41072 ( 4293) metal coordination : bond 0.00886 ( 26) metal coordination : angle 8.15761 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8310 (t80) REVERT: A 440 MET cc_start: 0.8930 (tpt) cc_final: 0.8667 (tpt) REVERT: A 1382 ASN cc_start: 0.8692 (t0) cc_final: 0.8104 (p0) REVERT: B 478 MET cc_start: 0.9292 (mmt) cc_final: 0.9072 (mmt) REVERT: B 719 MET cc_start: 0.9316 (mmm) cc_final: 0.8940 (tpp) REVERT: B 755 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8988 (pp) REVERT: B 929 MET cc_start: 0.7877 (ttt) cc_final: 0.7437 (ttt) REVERT: C 98 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8775 (p) REVERT: C 279 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7739 (ttm-80) REVERT: D 5 ASP cc_start: 0.8761 (t0) cc_final: 0.8248 (t0) REVERT: D 18 GLN cc_start: 0.8738 (tt0) cc_final: 0.8392 (tm-30) REVERT: D 22 ASP cc_start: 0.8754 (p0) cc_final: 0.7777 (p0) REVERT: E 152 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8566 (p) REVERT: H 37 MET cc_start: 0.8796 (mmm) cc_final: 0.8466 (mmm) REVERT: I 1 MET cc_start: 0.5651 (pmm) cc_final: 0.5380 (pmm) REVERT: L 27 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8020 (tm-30) REVERT: M 292 MET cc_start: -0.0731 (ptm) cc_final: -0.0996 (ptp) REVERT: N 116 MET cc_start: 0.9121 (tmm) cc_final: 0.8904 (tmm) REVERT: N 256 ARG cc_start: 0.8051 (ptp-170) cc_final: 0.7590 (ptp-170) REVERT: O 338 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8671 (mm) REVERT: O 398 MET cc_start: 0.8058 (mmm) cc_final: 0.7607 (mmp) REVERT: O 455 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8401 (tppt) REVERT: O 474 MET cc_start: 0.1315 (tmm) cc_final: 0.0954 (ptt) REVERT: P 310 MET cc_start: 0.8737 (tpp) cc_final: 0.8210 (mpp) REVERT: Q 29 ASP cc_start: 0.7875 (m-30) cc_final: 0.7413 (t0) REVERT: Q 71 MET cc_start: 0.8605 (mtm) cc_final: 0.8358 (mtm) REVERT: Q 82 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7121 (tm-30) REVERT: Q 111 MET cc_start: 0.8919 (mmm) cc_final: 0.8689 (mmp) outliers start: 82 outliers final: 43 residues processed: 318 average time/residue: 0.2499 time to fit residues: 136.5687 Evaluate side-chains 286 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain Q residue 31 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 255 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 492 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 375 optimal weight: 9.9990 chunk 452 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 407 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 ASN N 139 ASN ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 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 = 0.3630 r_free = 0.3630 target = 0.067094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043709 restraints weight = 178007.440| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 5.12 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 43436 Z= 0.208 Angle : 0.619 18.953 58838 Z= 0.306 Chirality : 0.044 0.179 6608 Planarity : 0.004 0.049 7427 Dihedral : 9.846 154.385 6180 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.64 % Allowed : 10.00 % Favored : 88.36 % Cbeta Deviations : 0.00 % 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: -0.37 (0.12), residues: 5180 helix: 0.70 (0.13), residues: 1851 sheet: -0.70 (0.18), residues: 746 loop : -0.74 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 100 TYR 0.024 0.001 TYR B 357 PHE 0.021 0.001 PHE O 148 TRP 0.017 0.001 TRP N 123 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00480 (43410) covalent geometry : angle 0.59953 (58802) hydrogen bonds : bond 0.03430 ( 1486) hydrogen bonds : angle 4.39802 ( 4293) metal coordination : bond 0.01025 ( 26) metal coordination : angle 6.17959 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 240 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8378 (t80) REVERT: A 440 MET cc_start: 0.8927 (tpt) cc_final: 0.8611 (tpt) REVERT: A 737 GLN cc_start: 0.8474 (tp40) cc_final: 0.7494 (pp30) REVERT: A 953 MET cc_start: 0.9114 (ttm) cc_final: 0.8903 (mtp) REVERT: A 1280 MET cc_start: 0.8103 (mpp) cc_final: 0.6980 (mpp) REVERT: A 1382 ASN cc_start: 0.8623 (t0) cc_final: 0.8079 (p0) REVERT: B 279 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 478 MET cc_start: 0.9285 (mmt) cc_final: 0.9069 (mmt) REVERT: B 719 MET cc_start: 0.9342 (mmm) cc_final: 0.8971 (tpp) REVERT: B 929 MET cc_start: 0.7872 (ttt) cc_final: 0.7403 (ttt) REVERT: C 98 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8783 (p) REVERT: C 173 MET cc_start: 0.9097 (mmm) cc_final: 0.8730 (mtp) REVERT: C 279 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7781 (ttm-80) REVERT: D 5 ASP cc_start: 0.8753 (t0) cc_final: 0.8257 (t0) REVERT: D 18 GLN cc_start: 0.8787 (tt0) cc_final: 0.8428 (tm-30) REVERT: D 22 ASP cc_start: 0.8746 (p0) cc_final: 0.7750 (p0) REVERT: E 94 MET cc_start: 0.8520 (ttt) cc_final: 0.8307 (ttp) REVERT: E 152 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8579 (p) REVERT: H 37 MET cc_start: 0.8747 (mmm) cc_final: 0.8420 (tpp) REVERT: J 57 GLU cc_start: 0.8508 (tp30) cc_final: 0.8288 (tp30) REVERT: L 27 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8021 (tm-30) REVERT: L 44 MET cc_start: 0.9156 (mmt) cc_final: 0.8533 (mmt) REVERT: N 132 MET cc_start: 0.8531 (tmm) cc_final: 0.8290 (tmm) REVERT: N 256 ARG cc_start: 0.8076 (ptp-170) cc_final: 0.7638 (ptp-170) REVERT: O 338 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8734 (mm) REVERT: O 398 MET cc_start: 0.8054 (mmm) cc_final: 0.7658 (mmp) REVERT: O 455 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8378 (tppt) REVERT: O 474 MET cc_start: 0.1482 (tmm) cc_final: 0.1171 (ptt) REVERT: P 310 MET cc_start: 0.8705 (tpp) cc_final: 0.8226 (mpp) REVERT: Q 29 ASP cc_start: 0.8008 (m-30) cc_final: 0.7534 (t0) REVERT: Q 40 ASP cc_start: 0.8257 (m-30) cc_final: 0.8020 (p0) REVERT: Q 71 MET cc_start: 0.8617 (mtm) cc_final: 0.8408 (mtm) outliers start: 76 outliers final: 48 residues processed: 297 average time/residue: 0.2486 time to fit residues: 127.0037 Evaluate side-chains 284 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 78 TYR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 338 LEU Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 168 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 73 optimal weight: 0.0270 chunk 494 optimal weight: 5.9990 chunk 450 optimal weight: 20.0000 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 HIS D 98 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS O 146 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 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 = 0.3662 r_free = 0.3662 target = 0.068163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044908 restraints weight = 177196.126| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.79 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 43436 Z= 0.105 Angle : 0.554 17.394 58838 Z= 0.272 Chirality : 0.042 0.177 6608 Planarity : 0.003 0.047 7427 Dihedral : 9.696 154.411 6178 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 1.36 % Allowed : 10.39 % Favored : 88.25 % Cbeta Deviations : 0.00 % 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: -0.11 (0.12), residues: 5180 helix: 0.96 (0.13), residues: 1846 sheet: -0.54 (0.19), residues: 742 loop : -0.62 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 128 TYR 0.016 0.001 TYR O 188 PHE 0.015 0.001 PHE P 210 TRP 0.012 0.001 TRP O 235 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00237 (43410) covalent geometry : angle 0.53835 (58802) hydrogen bonds : bond 0.02923 ( 1486) hydrogen bonds : angle 4.17799 ( 4293) metal coordination : bond 0.00485 ( 26) metal coordination : angle 5.37137 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 239 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7388 (m) REVERT: A 440 MET cc_start: 0.8861 (tpt) cc_final: 0.8541 (tpt) REVERT: A 1382 ASN cc_start: 0.8553 (t0) cc_final: 0.8097 (p0) REVERT: B 478 MET cc_start: 0.9301 (mmt) cc_final: 0.9022 (mmt) REVERT: B 719 MET cc_start: 0.9289 (mmm) cc_final: 0.8892 (tpp) REVERT: B 755 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8950 (pp) REVERT: B 929 MET cc_start: 0.7851 (ttt) cc_final: 0.7388 (ttt) REVERT: C 98 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 279 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7529 (ttm-80) REVERT: D 5 ASP cc_start: 0.8753 (t0) cc_final: 0.8236 (t0) REVERT: D 18 GLN cc_start: 0.8736 (tt0) cc_final: 0.8393 (tm-30) REVERT: D 22 ASP cc_start: 0.8736 (p0) cc_final: 0.7757 (p0) REVERT: D 100 MET cc_start: 0.8324 (mtp) cc_final: 0.8010 (ttt) REVERT: D 112 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: E 94 MET cc_start: 0.8532 (ttt) cc_final: 0.8303 (ttp) REVERT: H 37 MET cc_start: 0.8593 (mmm) cc_final: 0.8297 (tpp) REVERT: H 107 GLU cc_start: 0.8071 (mp0) cc_final: 0.7818 (mp0) REVERT: J 57 GLU cc_start: 0.8446 (tp30) cc_final: 0.8199 (tp30) REVERT: L 27 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8019 (tm-30) REVERT: L 44 MET cc_start: 0.9132 (mmt) cc_final: 0.8486 (mmt) REVERT: M 292 MET cc_start: -0.0869 (ptp) cc_final: -0.1385 (mtm) REVERT: N 256 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7607 (ptp-170) REVERT: O 398 MET cc_start: 0.8054 (mmm) cc_final: 0.7655 (mmp) REVERT: O 474 MET cc_start: 0.1003 (tmm) cc_final: 0.0537 (ptt) REVERT: P 232 MET cc_start: 0.6986 (mmm) cc_final: 0.6780 (mmm) REVERT: P 310 MET cc_start: 0.8730 (tpp) cc_final: 0.8228 (mpp) REVERT: Q 29 ASP cc_start: 0.8014 (m-30) cc_final: 0.7618 (t0) REVERT: Q 71 MET cc_start: 0.8521 (mtm) cc_final: 0.8293 (mtm) REVERT: Q 111 MET cc_start: 0.8568 (mmp) cc_final: 0.8146 (mmp) outliers start: 63 outliers final: 37 residues processed: 284 average time/residue: 0.2422 time to fit residues: 119.2984 Evaluate side-chains 272 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain P residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 209 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 407 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 chunk 503 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 276 GLN C 305 HIS I 81 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.066206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.042920 restraints weight = 179511.850| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.91 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 43436 Z= 0.258 Angle : 0.666 17.936 58838 Z= 0.327 Chirality : 0.045 0.181 6608 Planarity : 0.004 0.047 7427 Dihedral : 9.806 153.585 6178 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 1.38 % Allowed : 10.75 % Favored : 87.86 % Cbeta Deviations : 0.00 % 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: -0.12 (0.12), residues: 5180 helix: 0.97 (0.13), residues: 1844 sheet: -0.67 (0.18), residues: 758 loop : -0.60 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 369 TYR 0.030 0.002 TYR B 357 PHE 0.022 0.002 PHE B 326 TRP 0.015 0.001 TRP P 217 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00597 (43410) covalent geometry : angle 0.65095 (58802) hydrogen bonds : bond 0.03627 ( 1486) hydrogen bonds : angle 4.42487 ( 4293) metal coordination : bond 0.01321 ( 26) metal coordination : angle 5.69955 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8347 (t80) REVERT: A 440 MET cc_start: 0.8882 (tpt) cc_final: 0.8501 (mmt) REVERT: A 523 MET cc_start: 0.9444 (mmm) cc_final: 0.9165 (mtp) REVERT: A 1382 ASN cc_start: 0.8611 (t0) cc_final: 0.8082 (p0) REVERT: B 719 MET cc_start: 0.9367 (mmm) cc_final: 0.9013 (tpp) REVERT: B 755 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9037 (pp) REVERT: C 98 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8765 (p) REVERT: C 279 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7798 (ttm-80) REVERT: D 5 ASP cc_start: 0.8751 (t0) cc_final: 0.8244 (t0) REVERT: D 18 GLN cc_start: 0.8812 (tt0) cc_final: 0.8435 (tm-30) REVERT: D 22 ASP cc_start: 0.8749 (p0) cc_final: 0.7791 (p0) REVERT: E 94 MET cc_start: 0.8788 (ttt) cc_final: 0.8348 (ttp) REVERT: H 37 MET cc_start: 0.8601 (mmm) cc_final: 0.7801 (mmm) REVERT: I 42 LYS cc_start: 0.9323 (mmmm) cc_final: 0.8978 (mmtm) REVERT: J 57 GLU cc_start: 0.8514 (tp30) cc_final: 0.8230 (tp30) REVERT: J 58 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8500 (mmtm) REVERT: L 27 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8115 (tm-30) REVERT: N 256 ARG cc_start: 0.8161 (ptp-170) cc_final: 0.7730 (ptp-170) REVERT: O 270 MET cc_start: 0.9165 (mtm) cc_final: 0.8520 (mpp) REVERT: O 474 MET cc_start: 0.1412 (tmm) cc_final: 0.1031 (ptt) REVERT: P 203 MET cc_start: 0.9065 (tpp) cc_final: 0.8838 (mmt) REVERT: P 217 TRP cc_start: 0.7911 (t60) cc_final: 0.7566 (t60) REVERT: Q 29 ASP cc_start: 0.8071 (m-30) cc_final: 0.7660 (t0) REVERT: Q 71 MET cc_start: 0.8619 (mtm) cc_final: 0.8408 (mtm) REVERT: Q 82 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7378 (tm-30) outliers start: 64 outliers final: 43 residues processed: 281 average time/residue: 0.2422 time to fit residues: 118.3537 Evaluate side-chains 275 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 THR 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 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 92 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 189 optimal weight: 0.8980 chunk 318 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 383 optimal weight: 2.9990 chunk 142 optimal weight: 0.0070 chunk 514 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 794 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 HIS I 40 ASN I 81 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.067739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.044614 restraints weight = 176921.500| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.88 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 43436 Z= 0.106 Angle : 0.572 19.735 58838 Z= 0.278 Chirality : 0.042 0.179 6608 Planarity : 0.004 0.058 7427 Dihedral : 9.689 153.976 6178 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 1.08 % Allowed : 11.10 % Favored : 87.82 % Cbeta Deviations : 0.00 % 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: 0.13 (0.12), residues: 5180 helix: 1.20 (0.13), residues: 1835 sheet: -0.48 (0.19), residues: 737 loop : -0.50 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 369 TYR 0.020 0.001 TYR O 188 PHE 0.014 0.001 PHE B 662 TRP 0.015 0.001 TRP P 217 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00243 (43410) covalent geometry : angle 0.55391 (58802) hydrogen bonds : bond 0.02928 ( 1486) hydrogen bonds : angle 4.15399 ( 4293) metal coordination : bond 0.00511 ( 26) metal coordination : angle 5.79193 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 1.743 Fit side-chains REVERT: A 11 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7280 (m) REVERT: A 312 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8371 (t80) REVERT: A 440 MET cc_start: 0.8868 (tpt) cc_final: 0.8480 (mmt) REVERT: A 1382 ASN cc_start: 0.8595 (t0) cc_final: 0.8119 (p0) REVERT: B 478 MET cc_start: 0.9250 (mmt) cc_final: 0.9048 (mmt) REVERT: B 719 MET cc_start: 0.9281 (mmm) cc_final: 0.8855 (tpp) REVERT: B 755 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8959 (pp) REVERT: B 929 MET cc_start: 0.7919 (ttp) cc_final: 0.7693 (ttp) REVERT: C 98 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8824 (p) REVERT: C 279 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7610 (ttm-80) REVERT: D 5 ASP cc_start: 0.8819 (t0) cc_final: 0.8383 (t0) REVERT: D 18 GLN cc_start: 0.8759 (tt0) cc_final: 0.8420 (tm-30) REVERT: D 22 ASP cc_start: 0.8751 (p0) cc_final: 0.7760 (p0) REVERT: D 112 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: E 18 MET cc_start: 0.9328 (mmm) cc_final: 0.9104 (mmm) REVERT: E 94 MET cc_start: 0.8704 (ttt) cc_final: 0.8330 (ttt) REVERT: H 107 GLU cc_start: 0.8173 (mp0) cc_final: 0.7903 (mp0) REVERT: I 42 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8909 (mmtm) REVERT: J 57 GLU cc_start: 0.8470 (tp30) cc_final: 0.8197 (tp30) REVERT: L 27 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8081 (tm-30) REVERT: L 44 MET cc_start: 0.9141 (mmt) cc_final: 0.8472 (mmt) REVERT: N 132 MET cc_start: 0.8771 (tmm) cc_final: 0.8545 (ppp) REVERT: N 256 ARG cc_start: 0.8062 (ptp-170) cc_final: 0.7649 (ptp-170) REVERT: O 398 MET cc_start: 0.8367 (mmm) cc_final: 0.7916 (mmp) REVERT: O 474 MET cc_start: 0.1381 (tmm) cc_final: 0.1077 (ptt) REVERT: P 203 MET cc_start: 0.9020 (tpp) cc_final: 0.8667 (mmt) REVERT: P 217 TRP cc_start: 0.7807 (t60) cc_final: 0.7436 (t60) REVERT: P 310 MET cc_start: 0.8685 (tpp) cc_final: 0.8029 (mpp) REVERT: Q 29 ASP cc_start: 0.8075 (m-30) cc_final: 0.7696 (t0) REVERT: Q 71 MET cc_start: 0.8545 (mtm) cc_final: 0.8330 (mtm) REVERT: Q 82 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7503 (tm-30) outliers start: 50 outliers final: 37 residues processed: 270 average time/residue: 0.2458 time to fit residues: 114.6841 Evaluate side-chains 272 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 314 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 380 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 297 optimal weight: 0.0060 chunk 65 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 324 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 489 optimal weight: 9.9990 chunk 498 optimal weight: 6.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 HIS I 40 ASN I 81 GLN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 412 HIS ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 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 = 0.3623 r_free = 0.3623 target = 0.066624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043368 restraints weight = 178679.982| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.85 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 43436 Z= 0.197 Angle : 0.621 18.316 58838 Z= 0.302 Chirality : 0.043 0.180 6608 Planarity : 0.004 0.052 7427 Dihedral : 9.717 153.702 6178 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 1.15 % Allowed : 11.19 % Favored : 87.67 % Cbeta Deviations : 0.00 % 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: 0.08 (0.12), residues: 5180 helix: 1.19 (0.13), residues: 1854 sheet: -0.59 (0.18), residues: 758 loop : -0.52 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 369 TYR 0.021 0.001 TYR B 357 PHE 0.017 0.001 PHE B 326 TRP 0.017 0.001 TRP N 123 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00457 (43410) covalent geometry : angle 0.60328 (58802) hydrogen bonds : bond 0.03294 ( 1486) hydrogen bonds : angle 4.26591 ( 4293) metal coordination : bond 0.00997 ( 26) metal coordination : angle 6.06795 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 1.826 Fit side-chains REVERT: A 11 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7380 (m) REVERT: A 312 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (t80) REVERT: A 440 MET cc_start: 0.8899 (tpt) cc_final: 0.8510 (mmt) REVERT: A 523 MET cc_start: 0.9434 (mmm) cc_final: 0.9108 (mtp) REVERT: A 1382 ASN cc_start: 0.8636 (t0) cc_final: 0.8152 (p0) REVERT: B 478 MET cc_start: 0.9265 (mmt) cc_final: 0.9033 (mmt) REVERT: B 719 MET cc_start: 0.9339 (mmm) cc_final: 0.8946 (tpp) REVERT: B 755 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8978 (pp) REVERT: B 929 MET cc_start: 0.7946 (ttp) cc_final: 0.7647 (ttp) REVERT: C 98 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8720 (p) REVERT: C 279 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7799 (ttm-80) REVERT: D 5 ASP cc_start: 0.8790 (t0) cc_final: 0.8359 (t0) REVERT: D 18 GLN cc_start: 0.8818 (tt0) cc_final: 0.8448 (tm-30) REVERT: D 22 ASP cc_start: 0.8714 (p0) cc_final: 0.7735 (p0) REVERT: D 100 MET cc_start: 0.8371 (mtp) cc_final: 0.8085 (ttt) REVERT: D 112 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: E 18 MET cc_start: 0.9309 (mmm) cc_final: 0.9080 (mmm) REVERT: H 123 MET cc_start: 0.8958 (tmm) cc_final: 0.8746 (tmm) REVERT: I 42 LYS cc_start: 0.9319 (mmmm) cc_final: 0.8883 (mmtm) REVERT: J 57 GLU cc_start: 0.8540 (tp30) cc_final: 0.7971 (tp30) REVERT: L 27 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8087 (tm-30) REVERT: N 256 ARG cc_start: 0.8110 (ptp-170) cc_final: 0.7684 (ptp-170) REVERT: O 398 MET cc_start: 0.8293 (mmm) cc_final: 0.7867 (mmp) REVERT: O 474 MET cc_start: 0.1088 (tmm) cc_final: 0.0708 (ptt) REVERT: P 217 TRP cc_start: 0.7742 (t60) cc_final: 0.7424 (t60) REVERT: P 250 MET cc_start: 0.8337 (mmm) cc_final: 0.8122 (mmm) REVERT: P 310 MET cc_start: 0.8679 (tpp) cc_final: 0.8034 (mpp) REVERT: Q 29 ASP cc_start: 0.8063 (m-30) cc_final: 0.7723 (t0) REVERT: Q 71 MET cc_start: 0.8586 (mtm) cc_final: 0.8366 (mtm) REVERT: Q 82 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7531 (tm-30) REVERT: Q 111 MET cc_start: 0.8659 (mmp) cc_final: 0.8238 (mmp) outliers start: 53 outliers final: 41 residues processed: 263 average time/residue: 0.2433 time to fit residues: 111.1050 Evaluate side-chains 270 residues out of total 4622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 128 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 458 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 396 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 505 optimal weight: 40.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.066393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.043205 restraints weight = 178568.788| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 5.04 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 43436 Z= 0.176 Angle : 0.604 17.906 58838 Z= 0.294 Chirality : 0.043 0.190 6608 Planarity : 0.004 0.057 7427 Dihedral : 9.731 153.633 6178 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 1.21 % Allowed : 11.21 % Favored : 87.58 % Cbeta Deviations : 0.00 % 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: 0.12 (0.12), residues: 5180 helix: 1.22 (0.13), residues: 1855 sheet: -0.62 (0.18), residues: 763 loop : -0.48 (0.13), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 369 TYR 0.021 0.001 TYR O 188 PHE 0.015 0.001 PHE B 326 TRP 0.021 0.001 TRP N 123 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00410 (43410) covalent geometry : angle 0.58699 (58802) hydrogen bonds : bond 0.03198 ( 1486) hydrogen bonds : angle 4.22836 ( 4293) metal coordination : bond 0.00874 ( 26) metal coordination : angle 5.84766 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9298.45 seconds wall clock time: 161 minutes 20.08 seconds (9680.08 seconds total)