Starting phenix.real_space_refine on Sat Mar 7 11:27:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aea_11742/03_2026/7aea_11742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aea_11742/03_2026/7aea_11742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aea_11742/03_2026/7aea_11742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aea_11742/03_2026/7aea_11742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aea_11742/03_2026/7aea_11742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aea_11742/03_2026/7aea_11742.map" } resolution = 3.4 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= 0.006 sd= 0.051 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 26696 2.51 5 N 7362 2.21 5 O 8022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42422 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 10848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1381, 10848 Classifications: {'peptide': 1381} Link IDs: {'PTRANS': 65, 'TRANS': 1315} Chain breaks: 1 Chain: "B" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8680 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 2 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1001 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1509 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 849 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3025 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 20, 'TRANS': 354} Chain breaks: 3 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 69 100.561 69.186 119.530 1.00138.98 S ATOM 613 SG CYS A 79 96.626 67.337 117.966 1.00117.49 S ATOM 854 SG CYS A 109 68.807 96.710 144.517 1.00139.56 S ATOM 876 SG CYS A 112 68.409 93.394 147.173 1.00145.21 S ATOM 1245 SG CYS A 156 64.609 94.360 146.661 1.00155.76 S ATOM 1271 SG CYS A 159 67.245 96.530 148.509 1.00154.28 S ATOM 19115 SG CYS B1080 83.603 62.718 128.839 1.00109.77 S ATOM 19134 SG CYS B1083 83.027 66.617 129.520 1.00111.92 S ATOM 19200 SG CYS B1092 87.064 64.664 129.082 1.00118.58 S ATOM 19228 SG CYS B1095 84.891 64.801 132.607 1.00124.09 S ATOM 28343 SG CYS I 5 55.474 148.262 109.401 1.00108.01 S ATOM 28360 SG CYS I 8 58.973 146.325 110.608 1.00106.25 S ATOM 28491 SG CYS I 25 56.501 144.860 112.773 1.00119.74 S ATOM 28512 SG CYS I 28 56.731 148.542 112.753 1.00121.15 S ATOM 29206 SG CYS J 7 87.619 75.729 47.961 1.00 56.51 S ATOM 29230 SG CYS J 10 86.785 72.490 45.277 1.00 57.09 S ATOM 29494 SG CYS J 44 84.231 75.449 46.111 1.00 57.89 S ATOM 29500 SG CYS J 45 87.688 75.690 43.873 1.00 59.64 S ATOM 30589 SG CYS L 19 121.218 92.227 70.133 1.00 85.36 S ATOM 30608 SG CYS L 22 123.196 93.118 67.218 1.00 92.64 S ATOM 30725 SG CYS L 36 124.845 92.985 70.453 1.00 97.36 S Time building chain proxies: 8.72, per 1000 atoms: 0.21 Number of scatterers: 42422 At special positions: 0 Unit cell: (141.75, 184.8, 205.8, 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 8022 8.00 N 7362 7.00 C 26696 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " 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 A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 25 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 24 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9824 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 56 sheets defined 37.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.858A pdb=" N GLY A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.566A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 4.200A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.949A pdb=" N PHE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.797A pdb=" N GLU A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.755A pdb=" N LEU A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.697A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 277 through 299 removed outlier: 3.563A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 removed outlier: 3.747A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.795A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.518A pdb=" N MET A 440 " --> pdb=" O ASN A 436 " (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: 3.992A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 521 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 597 through 606 removed outlier: 4.260A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.088A 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 671 Processing helix chain 'A' and resid 672 through 695 removed outlier: 3.915A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.777A pdb=" N ASN A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.602A pdb=" N VAL A 703 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 733 removed outlier: 3.573A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 765 removed outlier: 3.671A pdb=" N LEU A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 760 " --> pdb=" O LEU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.774A pdb=" N ILE A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 832 removed outlier: 4.093A pdb=" N GLY A 832 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 864 removed outlier: 3.776A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 880 removed outlier: 3.884A pdb=" N GLY A 869 " --> pdb=" O THR A 865 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET A 871 " --> pdb=" O GLU A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.574A pdb=" N GLY A 904 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 removed outlier: 4.010A 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 956 through 961 removed outlier: 3.886A pdb=" N CYS A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 987 removed outlier: 3.635A pdb=" N LEU A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 removed outlier: 3.616A 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 1048 removed outlier: 3.741A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 3.639A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.625A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.587A pdb=" N ALA A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A1100 " --> pdb=" O ASP A1096 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A1105 " --> pdb=" O VAL A1101 " (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 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 3.649A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 removed outlier: 3.713A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1246 removed outlier: 4.188A 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 1258 removed outlier: 3.566A pdb=" N VAL A1254 " --> pdb=" O ASN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1277 Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 4.102A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1312 Processing helix chain 'A' and resid 1314 through 1320 Processing helix chain 'A' and resid 1323 through 1334 removed outlier: 3.848A pdb=" N HIS A1327 " --> pdb=" O LYS A1323 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1350 removed outlier: 3.869A pdb=" N ILE A1348 " --> pdb=" O SER A1344 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 3.617A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.805A 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 'B' and resid 24 through 27 removed outlier: 4.455A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 27' Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.648A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 61 removed outlier: 3.599A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.568A pdb=" N CYS B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.641A 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: 3.680A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.899A pdb=" N LEU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.752A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.557A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.701A pdb=" N LYS B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET B 406 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 410 removed outlier: 3.980A pdb=" N GLN B 410 " --> pdb=" O ARG B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 407 through 410' Processing helix chain 'B' and resid 411 through 422 removed outlier: 3.734A pdb=" N GLY B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 removed outlier: 3.707A pdb=" N ALA B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.609A pdb=" N TRP B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 4.559A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 4.008A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.661A 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 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.602A pdb=" N ASN B 639 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.643A pdb=" N ILE B 650 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.511A pdb=" N LEU B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.924A pdb=" N LEU B 671 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.803A pdb=" N ASN B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 3.715A pdb=" N GLU B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.689A 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 803 through 807 removed outlier: 3.546A pdb=" N GLU B 807 " --> pdb=" O TRP B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 954 removed outlier: 3.807A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 979 removed outlier: 3.669A pdb=" N LEU B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 977 " --> pdb=" O CYS B 973 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 979 " --> pdb=" O ASP B 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 972 through 979' Processing helix chain 'B' and resid 1038 through 1042 Processing helix chain 'B' and resid 1051 through 1058 removed outlier: 3.751A pdb=" N GLY B1057 " --> pdb=" O ASP B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1069 Processing helix chain 'B' and resid 1069 through 1073 Processing helix chain 'B' and resid 1108 through 1112 Processing helix chain 'B' and resid 1112 through 1120 removed outlier: 4.022A pdb=" N GLN B1118 " --> pdb=" O PHE B1114 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 removed outlier: 4.099A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.528A 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: 3.831A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.602A pdb=" N LEU C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 281' Processing helix chain 'C' and resid 317 through 338 removed outlier: 3.530A pdb=" N LEU C 321 " --> pdb=" O PRO C 317 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 27 removed outlier: 3.533A pdb=" N THR D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 3.757A pdb=" N THR D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 73 removed outlier: 3.660A pdb=" N GLU D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 77 removed outlier: 4.271A 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: 3.625A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 88 " --> pdb=" O LEU D 84 " (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 122 removed outlier: 3.503A pdb=" N HIS D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.890A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 25 " --> pdb=" O CYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.571A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.963A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.886A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.841A pdb=" N GLN E 169 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 166 through 170' Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.875A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.791A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.804A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.552A pdb=" N LEU I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY I 54 " --> pdb=" O ASP I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 54' Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.631A pdb=" N ALA J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.643A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.861A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.632A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 127 Processing helix chain 'M' and resid 70 through 82 removed outlier: 4.028A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 154 removed outlier: 4.049A pdb=" N ASP M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 201 Processing helix chain 'M' and resid 215 through 221 removed outlier: 4.042A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS M 220 " --> pdb=" O SER M 216 " (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 282 through 289 Processing helix chain 'M' and resid 293 through 301 removed outlier: 3.688A pdb=" N LEU M 297 " --> pdb=" O PRO M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 316 removed outlier: 3.957A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 333 Processing helix chain 'M' and resid 349 through 363 removed outlier: 3.591A pdb=" N ARG M 353 " --> pdb=" O LEU M 349 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 375 Processing helix chain 'M' and resid 381 through 387 Processing helix chain 'M' and resid 417 through 422 removed outlier: 3.955A pdb=" N MET M 421 " --> pdb=" O GLN M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 124 removed outlier: 3.778A pdb=" N TRP N 123 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.869A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 257 removed outlier: 3.800A pdb=" N ARG N 256 " --> pdb=" O ALA N 252 " (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 394 Processing helix chain 'O' and resid 3 through 17 removed outlier: 3.882A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS O 16 " --> pdb=" O LEU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 31 removed outlier: 3.885A pdb=" N HIS O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU O 28 " --> pdb=" O ILE O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 42 removed outlier: 3.759A pdb=" N ALA O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 removed outlier: 3.546A pdb=" N VAL O 50 " --> pdb=" O SER O 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS O 51 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL O 56 " --> pdb=" O LYS O 52 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 84 Processing helix chain 'O' and resid 87 through 99 removed outlier: 3.657A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS O 96 " --> pdb=" O ILE O 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR O 97 " --> pdb=" O TYR O 93 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 114 removed outlier: 3.652A pdb=" N LEU O 105 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL O 107 " --> pdb=" O GLY O 103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 129 removed outlier: 3.786A pdb=" N VAL O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 4.171A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER O 145 " --> pdb=" O TYR O 141 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG O 150 " --> pdb=" O ASN O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 259 removed outlier: 3.572A pdb=" N ASP O 248 " --> pdb=" O GLN O 244 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN O 249 " --> pdb=" O HIS O 245 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA O 250 " --> pdb=" O PHE O 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER O 253 " --> pdb=" O GLN O 249 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG O 258 " --> pdb=" O ALA O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 274 removed outlier: 4.024A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET O 273 " --> pdb=" O THR O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 removed outlier: 4.203A pdb=" N ARG O 295 " --> pdb=" O ASN O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 315 removed outlier: 3.522A pdb=" N LEU O 312 " --> pdb=" O LEU O 308 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR O 313 " --> pdb=" O ASP O 309 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 353 removed outlier: 3.639A pdb=" N VAL O 353 " --> pdb=" O THR O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 353 through 359 Processing helix chain 'O' and resid 359 through 372 removed outlier: 3.542A pdb=" N ALA O 363 " --> pdb=" O GLY O 359 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 384 removed outlier: 3.593A pdb=" N VAL O 380 " --> pdb=" O GLU O 376 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU O 381 " --> pdb=" O GLN O 377 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP O 382 " --> pdb=" O LYS O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 390 through 400 removed outlier: 3.951A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET O 398 " --> pdb=" O MET O 394 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU O 399 " --> pdb=" O LEU O 395 " (cutoff:3.500A) Processing helix chain 'O' and resid 429 through 454 removed outlier: 3.658A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 removed outlier: 3.507A pdb=" N LEU O 461 " --> pdb=" O ASN O 457 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL O 467 " --> pdb=" O LYS O 463 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU O 468 " --> pdb=" O SER O 464 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 495 through 530 removed outlier: 3.630A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS O 508 " --> pdb=" O ARG O 504 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA O 511 " --> pdb=" O ASN O 507 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU O 522 " --> pdb=" O GLU O 518 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR O 530 " --> pdb=" O TYR O 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 197 removed outlier: 3.525A pdb=" N GLU P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS P 186 " --> pdb=" O GLN P 182 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER P 190 " --> pdb=" O LYS P 186 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS P 191 " --> pdb=" O PHE P 187 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA P 192 " --> pdb=" O LEU P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 208 removed outlier: 3.653A pdb=" N ASN P 207 " --> pdb=" O MET P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 224 removed outlier: 3.808A pdb=" N TYR P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE P 220 " --> pdb=" O VAL P 216 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS P 221 " --> pdb=" O TRP P 217 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU P 222 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY P 224 " --> pdb=" O ILE P 220 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 239 removed outlier: 4.196A pdb=" N THR P 237 " --> pdb=" O GLU P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 245 Processing helix chain 'P' and resid 303 through 306 Processing helix chain 'P' and resid 307 through 314 removed outlier: 3.516A pdb=" N THR P 311 " --> pdb=" O CYS P 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 20 Processing helix chain 'Q' and resid 51 through 69 removed outlier: 3.939A pdb=" N TYR Q 56 " --> pdb=" O GLU Q 52 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N MET Q 57 " --> pdb=" O GLY Q 53 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR Q 67 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.854A pdb=" N MET Q 110 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET Q 111 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 107 through 111' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.988A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N LEU G 48 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N PHE G 77 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ASP G 50 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL G 75 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR G 52 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ARG G 73 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU G 54 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N HIS G 71 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP G 56 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS G 69 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE G 72 " --> pdb=" O MET G 7 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 2 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.988A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA G 57 " --> pdb=" O HIS A1364 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A1362 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE F 105 " --> pdb=" O LEU A1363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 7.117A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.881A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 84 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.340A 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: 3.736A pdb=" N LYS A 167 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 380 removed outlier: 4.027A pdb=" N PHE A 488 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.639A pdb=" N GLU A 451 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 616 through 620 removed outlier: 6.731A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.587A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 891 " --> pdb=" O CYS A 883 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1209 through 1214 removed outlier: 3.859A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 7.536A 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: 3.542A pdb=" N LYS A1131 " --> pdb=" O TYR A1116 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A1119 " --> pdb=" O ASN I 40 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN I 40 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL I 38 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.644A pdb=" N LEU B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.644A pdb=" N LEU B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 86 through 88 removed outlier: 4.042A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.501A pdb=" N VAL B 203 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC4, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AC5, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC6, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 549 removed outlier: 5.761A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 573 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.679A pdb=" N LYS B 773 " --> pdb=" O LEU B 885 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 775 " --> pdb=" O MET B 883 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 737 through 741 Processing sheet with id=AD1, first strand: chain 'B' and resid 755 through 758 removed outlier: 5.652A pdb=" N LEU B 755 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 909 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 911 " --> pdb=" O LEU B 757 " (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 826 through 828 removed outlier: 6.806A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 986 through 987 Processing sheet with id=AD5, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.410A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B1077 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 57 removed outlier: 5.788A pdb=" N VAL C 51 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL C 66 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL C 53 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP C 64 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 60 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 63 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C 306 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ARG C 303 " --> pdb=" O PRO C 237 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N HIS C 305 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU C 235 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 307 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR C 233 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 212 through 217 removed outlier: 6.801A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.729A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.639A 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: 3.591A pdb=" N VAL C 168 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.893A 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 removed outlier: 3.565A pdb=" N GLU C 263 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 274 " --> pdb=" O GLU C 263 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 72 through 75 removed outlier: 6.045A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 removed outlier: 4.074A 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: 3.999A 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: 5.555A pdb=" N VAL G 152 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER G 189 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER G 156 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR G 185 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N PHE G 104 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N LEU G 186 " --> pdb=" O PHE G 104 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP G 106 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY G 188 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU G 108 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP G 106 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL G 99 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU G 108 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL G 97 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS G 90 " --> pdb=" O HIS G 98 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 150 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 128 through 129 removed outlier: 3.606A pdb=" N TRP G 129 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP G 139 " --> pdb=" O TRP G 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.739A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN H 126 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE H 6 " --> pdb=" O ILE H 60 " (cutoff:3.500A) 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: 3.645A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 27 through 31 removed outlier: 6.859A pdb=" N ARG K 83 " --> pdb=" O CYS K 68 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS K 68 " --> pdb=" O ARG K 83 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN K 85 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 370 through 387 removed outlier: 6.932A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU M 59 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA M 47 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU M 57 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU N 357 " --> pdb=" O TYR M 30 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE N 356 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS N 380 " --> pdb=" O PHE N 356 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU N 266 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS M 125 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 318 through 320 Processing sheet with id=AF6, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AF7, first strand: chain 'O' and resid 34 through 35 removed outlier: 3.576A pdb=" N GLN O 34 " --> pdb=" O TYR O 75 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (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 'P' and resid 211 through 212 1351 hydrogen bonds defined for protein. 3813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.57 Time building geometry restraints manager: 4.51 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: 17652 1.43 - 1.64: 25193 1.64 - 1.86: 446 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 43303 Sorted by residual: bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.336 1.397 -0.061 9.80e-03 1.04e+04 3.88e+01 bond pdb=" CA TYR A1187 " pdb=" C TYR A1187 " ideal model delta sigma weight residual 1.524 1.609 -0.085 2.25e-02 1.98e+03 1.43e+01 bond pdb=" C GLU A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" C GLN G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.23e-02 6.61e+03 5.91e+00 bond pdb=" C LEU N 275 " pdb=" N PRO N 276 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.65e+00 ... (remaining 43298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 57904 3.01 - 6.02: 670 6.02 - 9.03: 69 9.03 - 12.04: 8 12.04 - 15.05: 2 Bond angle restraints: 58653 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 121.97 137.02 -15.05 1.80e+00 3.09e-01 6.99e+01 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 120.10 -10.76 2.08e+00 2.31e-01 2.68e+01 angle pdb=" C ASN B 52 " pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta sigma weight residual 122.77 117.61 5.16 1.05e+00 9.07e-01 2.42e+01 angle pdb=" N SER N 368 " pdb=" CA SER N 368 " pdb=" C SER N 368 " ideal model delta sigma weight residual 111.28 116.54 -5.26 1.09e+00 8.42e-01 2.32e+01 angle pdb=" C ILE A1153 " pdb=" N CYS A1154 " pdb=" CA CYS A1154 " ideal model delta sigma weight residual 123.93 131.32 -7.39 1.54e+00 4.22e-01 2.30e+01 ... (remaining 58648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.33: 26046 30.33 - 60.66: 440 60.66 - 90.99: 31 90.99 - 121.32: 0 121.32 - 151.65: 2 Dihedral angle restraints: 26519 sinusoidal: 11327 harmonic: 15192 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 -123.22 -56.78 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA VAL M 366 " pdb=" C VAL M 366 " pdb=" N VAL M 367 " pdb=" CA VAL M 367 " ideal model delta harmonic sigma weight residual -180.00 -127.97 -52.03 0 5.00e+00 4.00e-02 1.08e+02 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 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 26516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5121 0.060 - 0.120: 1217 0.120 - 0.180: 228 0.180 - 0.240: 22 0.240 - 0.300: 5 Chirality restraints: 6593 Sorted by residual: chirality pdb=" CB ILE A 473 " pdb=" CA ILE A 473 " pdb=" CG1 ILE A 473 " pdb=" CG2 ILE A 473 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 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 2.19 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB ILE J 3 " pdb=" CA ILE J 3 " pdb=" CG1 ILE J 3 " pdb=" CG2 ILE J 3 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 6590 not shown) Planarity restraints: 7406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1196 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A1197 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1197 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1197 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 263 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO M 264 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO M 264 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 264 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 467 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO B 468 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " 0.039 5.00e-02 4.00e+02 ... (remaining 7403 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 10 2.32 - 2.97: 17586 2.97 - 3.61: 58295 3.61 - 4.26: 94967 4.26 - 4.90: 156232 Nonbonded interactions: 327090 Sorted by model distance: nonbonded pdb=" O3' G R 19 " pdb="MG MG R 101 " model vdw 1.679 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG R 101 " model vdw 2.088 2.170 nonbonded pdb=" O PRO I 44 " pdb=" OG SER I 86 " model vdw 2.268 3.040 nonbonded pdb=" O SER A 697 " pdb=" OG SER A 776 " model vdw 2.271 3.040 nonbonded pdb=" O MET A 646 " pdb=" OG SER H 117 " model vdw 2.275 3.040 ... (remaining 327085 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: 2.410 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: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 48.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.885 43328 Z= 0.392 Angle : 1.064 56.055 58689 Z= 0.535 Chirality : 0.054 0.300 6593 Planarity : 0.007 0.073 7406 Dihedral : 11.118 151.650 16695 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 0.28 % Allowed : 2.60 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.32 (0.09), residues: 5164 helix: -3.73 (0.07), residues: 1672 sheet: -2.06 (0.18), residues: 689 loop : -2.52 (0.10), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 22 TYR 0.043 0.003 TYR B1003 PHE 0.033 0.003 PHE C 308 TRP 0.024 0.003 TRP B 73 HIS 0.013 0.002 HIS O 374 Details of bonding type rmsd covalent geometry : bond 0.00528 (43303) covalent geometry : angle 0.91588 (58653) hydrogen bonds : bond 0.25305 ( 1329) hydrogen bonds : angle 8.83979 ( 3813) metal coordination : bond 0.41084 ( 25) metal coordination : angle 21.90560 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 622 time to evaluate : 1.624 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8918 (mmm) cc_final: 0.7717 (ptt) REVERT: A 305 MET cc_start: 0.8323 (mtp) cc_final: 0.8020 (mmp) REVERT: A 912 MET cc_start: 0.8564 (mmt) cc_final: 0.8157 (mmm) REVERT: A 1027 MET cc_start: 0.8752 (tpp) cc_final: 0.8491 (tpp) REVERT: A 1196 LEU cc_start: 0.9310 (tp) cc_final: 0.9005 (mm) REVERT: A 1378 ILE cc_start: 0.7956 (mt) cc_final: 0.7710 (mt) REVERT: D 7 ASN cc_start: 0.7104 (p0) cc_final: 0.6752 (p0) REVERT: G 127 TRP cc_start: 0.3821 (m100) cc_final: 0.3447 (m100) REVERT: I 79 PHE cc_start: 0.6879 (p90) cc_final: 0.6430 (p90) REVERT: I 80 MET cc_start: 0.8892 (tpt) cc_final: 0.8584 (mmm) REVERT: I 84 THR cc_start: 0.6407 (p) cc_final: 0.6184 (p) REVERT: M 286 MET cc_start: 0.7723 (tpp) cc_final: 0.7222 (tpp) REVERT: N 113 PRO cc_start: 0.8382 (Cg_exo) cc_final: 0.7383 (Cg_endo) REVERT: O 55 CYS cc_start: 0.9021 (p) cc_final: 0.8689 (p) REVERT: P 240 ASN cc_start: 0.8187 (m110) cc_final: 0.7891 (m110) REVERT: P 269 LEU cc_start: 0.7027 (mt) cc_final: 0.6443 (mt) outliers start: 13 outliers final: 2 residues processed: 635 average time/residue: 0.2871 time to fit residues: 286.5877 Evaluate side-chains 317 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 261 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 114 HIS A 124 GLN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 476 HIS A 616 ASN A 662 ASN A 885 GLN A 927 ASN A1180 ASN A1190 GLN A1213 HIS A1239 HIS B 320 HIS B 346 GLN B 501 HIS B 602 GLN B 636 ASN B 683 ASN B 758 ASN B 901 HIS B 903 GLN B1100 HIS C 108 HIS C 305 HIS E 98 ASN G 115 GLN H 76 ASN I 18 GLN I 40 ASN K 74 HIS K 81 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 GLN M 29 GLN M 76 GLN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 GLN M 288 ASN M 315 GLN N 106 HIS N 111 GLN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN O 113 ASN O 146 ASN O 155 HIS O 310 GLN O 515 GLN P 181 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.080314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054851 restraints weight = 160989.583| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.80 r_work: 0.2914 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43328 Z= 0.186 Angle : 0.669 17.695 58689 Z= 0.338 Chirality : 0.044 0.191 6593 Planarity : 0.005 0.062 7406 Dihedral : 10.276 157.319 6165 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 1.24 % Allowed : 6.57 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.92 (0.10), residues: 5164 helix: -1.94 (0.11), residues: 1753 sheet: -1.66 (0.18), residues: 682 loop : -1.99 (0.10), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 70 TYR 0.025 0.002 TYR D 14 PHE 0.029 0.002 PHE A 462 TRP 0.025 0.002 TRP A 337 HIS 0.013 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00417 (43303) covalent geometry : angle 0.63995 (58653) hydrogen bonds : bond 0.04713 ( 1329) hydrogen bonds : angle 5.47822 ( 3813) metal coordination : bond 0.01550 ( 25) metal coordination : angle 7.88319 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 333 time to evaluate : 1.471 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: A 281 MET cc_start: 0.8711 (mmm) cc_final: 0.7680 (ptt) REVERT: A 1027 MET cc_start: 0.9139 (tpp) cc_final: 0.8639 (tpp) REVERT: A 1196 LEU cc_start: 0.9164 (tp) cc_final: 0.8961 (mm) REVERT: A 1228 GLU cc_start: 0.8331 (tt0) cc_final: 0.7591 (tm-30) REVERT: A 1311 MET cc_start: 0.8905 (mtm) cc_final: 0.8666 (mtm) REVERT: B 208 HIS cc_start: 0.7847 (p-80) cc_final: 0.6937 (p90) REVERT: C 98 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8910 (p) REVERT: D 76 HIS cc_start: 0.9277 (OUTLIER) cc_final: 0.8590 (t-90) REVERT: E 56 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7871 (p) REVERT: E 72 MET cc_start: 0.8319 (ttp) cc_final: 0.8034 (ttm) REVERT: F 83 LEU cc_start: 0.9146 (pt) cc_final: 0.8900 (pp) REVERT: G 7 MET cc_start: 0.8525 (mtm) cc_final: 0.8300 (ttm) REVERT: G 9 ASP cc_start: 0.8379 (t0) cc_final: 0.8125 (t0) REVERT: G 120 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.6230 (m-80) REVERT: G 127 TRP cc_start: 0.3481 (m100) cc_final: 0.3146 (m100) REVERT: I 79 PHE cc_start: 0.6912 (p90) cc_final: 0.6584 (p90) REVERT: I 91 MET cc_start: 0.5522 (ttp) cc_final: 0.5082 (ttm) REVERT: L 25 GLU cc_start: 0.8792 (mp0) cc_final: 0.8541 (mt-10) REVERT: L 44 MET cc_start: 0.9445 (mmt) cc_final: 0.8984 (mmm) REVERT: M 286 MET cc_start: 0.7681 (tpp) cc_final: 0.7226 (tpp) REVERT: M 292 MET cc_start: 0.1783 (ptt) cc_final: 0.1554 (ptt) REVERT: M 394 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5758 (mt) REVERT: O 55 CYS cc_start: 0.9061 (p) cc_final: 0.8776 (p) REVERT: P 200 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7119 (pm20) REVERT: Q 68 MET cc_start: 0.7847 (tpt) cc_final: 0.7351 (tpt) REVERT: Q 92 MET cc_start: 0.7106 (ptm) cc_final: 0.6487 (ptp) REVERT: Q 110 MET cc_start: 0.5823 (mmm) cc_final: 0.5307 (mmm) outliers start: 57 outliers final: 29 residues processed: 377 average time/residue: 0.2609 time to fit residues: 163.7728 Evaluate side-chains 320 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 301 LEU Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 285 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 449 optimal weight: 8.9990 chunk 426 optimal weight: 9.9990 chunk 459 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 292 optimal weight: 20.0000 chunk 330 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 316 GLN A 738 GLN A 836 ASN A1286 HIS ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 183 GLN B 215 ASN B 289 ASN B 677 HIS ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS H 126 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 GLN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 445 ASN O 457 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.077914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052382 restraints weight = 161569.290| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.76 r_work: 0.2844 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 43328 Z= 0.283 Angle : 0.699 17.421 58689 Z= 0.351 Chirality : 0.045 0.180 6593 Planarity : 0.005 0.055 7406 Dihedral : 10.170 156.845 6165 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 1.82 % Allowed : 7.51 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.09 (0.11), residues: 5164 helix: -0.94 (0.12), residues: 1775 sheet: -1.55 (0.18), residues: 699 loop : -1.61 (0.11), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 463 TYR 0.029 0.002 TYR B 357 PHE 0.030 0.002 PHE I 94 TRP 0.025 0.002 TRP A 337 HIS 0.012 0.002 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00644 (43303) covalent geometry : angle 0.67899 (58653) hydrogen bonds : bond 0.04372 ( 1329) hydrogen bonds : angle 5.10983 ( 3813) metal coordination : bond 0.01199 ( 25) metal coordination : angle 6.80827 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 1.724 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: A 281 MET cc_start: 0.8734 (mmm) cc_final: 0.8411 (ptt) REVERT: A 1196 LEU cc_start: 0.9226 (tp) cc_final: 0.8915 (mm) REVERT: A 1228 GLU cc_start: 0.8502 (tt0) cc_final: 0.7862 (tm-30) REVERT: A 1384 PHE cc_start: 0.7327 (m-10) cc_final: 0.7049 (m-10) REVERT: A 1388 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5391 (mm) REVERT: B 611 MET cc_start: 0.9240 (mmm) cc_final: 0.8911 (mmm) REVERT: C 98 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8756 (p) REVERT: D 76 HIS cc_start: 0.9251 (OUTLIER) cc_final: 0.8682 (t-90) REVERT: E 56 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.8011 (p) REVERT: E 152 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7940 (p) REVERT: F 83 LEU cc_start: 0.9211 (pt) cc_final: 0.8906 (pp) REVERT: G 7 MET cc_start: 0.8435 (mtm) cc_final: 0.8126 (ttm) REVERT: G 9 ASP cc_start: 0.8505 (t0) cc_final: 0.8185 (t70) REVERT: G 120 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: I 80 MET cc_start: 0.8251 (tpp) cc_final: 0.7791 (tpp) REVERT: I 91 MET cc_start: 0.5371 (ttp) cc_final: 0.5146 (ttm) REVERT: K 47 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8638 (tp30) REVERT: L 25 GLU cc_start: 0.8979 (mp0) cc_final: 0.8733 (mt-10) REVERT: L 44 MET cc_start: 0.9325 (mmt) cc_final: 0.8966 (mmm) REVERT: M 60 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8138 (tpp) REVERT: M 394 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5227 (mt) REVERT: N 350 MET cc_start: 0.8667 (tpp) cc_final: 0.8433 (mpp) REVERT: O 55 CYS cc_start: 0.9065 (p) cc_final: 0.8781 (p) REVERT: O 133 MET cc_start: 0.2714 (ptt) cc_final: 0.2267 (ptt) REVERT: O 139 MET cc_start: 0.7060 (tpt) cc_final: 0.6754 (tpt) REVERT: O 455 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8163 (ttpt) REVERT: P 282 LEU cc_start: 0.7228 (tp) cc_final: 0.6903 (tp) REVERT: Q 68 MET cc_start: 0.7996 (tpt) cc_final: 0.7388 (tpt) REVERT: Q 92 MET cc_start: 0.7205 (ptm) cc_final: 0.6632 (ptp) REVERT: Q 110 MET cc_start: 0.5989 (mmm) cc_final: 0.5580 (mmm) outliers start: 84 outliers final: 39 residues processed: 359 average time/residue: 0.2614 time to fit residues: 157.1838 Evaluate side-chains 318 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 15 ASN Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 70 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 350 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 498 optimal weight: 7.9990 chunk 420 optimal weight: 9.9990 chunk 328 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 623 GLN ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 129 ASN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.078210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052808 restraints weight = 160826.551| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.75 r_work: 0.2857 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43328 Z= 0.195 Angle : 0.609 16.579 58689 Z= 0.305 Chirality : 0.043 0.172 6593 Planarity : 0.004 0.060 7406 Dihedral : 10.012 157.848 6165 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 1.35 % Allowed : 8.55 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.61 (0.11), residues: 5164 helix: -0.39 (0.12), residues: 1768 sheet: -1.32 (0.19), residues: 675 loop : -1.43 (0.11), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 54 TYR 0.019 0.001 TYR B 357 PHE 0.021 0.001 PHE A 462 TRP 0.025 0.001 TRP A 337 HIS 0.010 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00444 (43303) covalent geometry : angle 0.59162 (58653) hydrogen bonds : bond 0.03666 ( 1329) hydrogen bonds : angle 4.81750 ( 3813) metal coordination : bond 0.00943 ( 25) metal coordination : angle 5.93888 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.8921 (mmm) cc_final: 0.8359 (ptt) REVERT: A 646 MET cc_start: 0.9284 (mmm) cc_final: 0.8497 (mmm) REVERT: A 1151 TYR cc_start: 0.8339 (t80) cc_final: 0.8054 (t80) REVERT: A 1384 PHE cc_start: 0.7244 (m-10) cc_final: 0.6991 (m-80) REVERT: D 40 GLN cc_start: 0.8731 (tt0) cc_final: 0.8489 (mp10) REVERT: D 51 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6620 (pttm) REVERT: D 76 HIS cc_start: 0.9215 (OUTLIER) cc_final: 0.8680 (t-90) REVERT: E 55 ARG cc_start: 0.8601 (mpt90) cc_final: 0.8367 (tmm160) REVERT: E 72 MET cc_start: 0.8414 (ttp) cc_final: 0.7717 (mtp) REVERT: E 141 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8570 (mp0) REVERT: E 152 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7902 (p) REVERT: F 83 LEU cc_start: 0.9192 (pt) cc_final: 0.8949 (pp) REVERT: G 7 MET cc_start: 0.8424 (mtm) cc_final: 0.8141 (ttm) REVERT: G 9 ASP cc_start: 0.8605 (t0) cc_final: 0.8251 (t70) REVERT: G 120 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: I 91 MET cc_start: 0.5601 (ttp) cc_final: 0.5331 (tpp) REVERT: L 25 GLU cc_start: 0.8987 (mp0) cc_final: 0.8696 (mt-10) REVERT: L 44 MET cc_start: 0.9280 (mmt) cc_final: 0.8939 (mmm) REVERT: M 282 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.7873 (mm) REVERT: M 286 MET cc_start: 0.8289 (mmm) cc_final: 0.6499 (tpp) REVERT: M 314 ILE cc_start: 0.3515 (mt) cc_final: 0.3197 (mt) REVERT: M 394 ILE cc_start: 0.5527 (OUTLIER) cc_final: 0.5121 (mt) REVERT: N 116 MET cc_start: 0.8326 (mmt) cc_final: 0.7939 (mpp) REVERT: O 133 MET cc_start: 0.3131 (ptt) cc_final: 0.2788 (ptt) REVERT: O 139 MET cc_start: 0.7052 (tpt) cc_final: 0.6753 (tpt) REVERT: O 248 ASP cc_start: 0.8729 (p0) cc_final: 0.8273 (m-30) REVERT: O 531 MET cc_start: 0.7411 (ttt) cc_final: 0.7166 (mtp) REVERT: P 282 LEU cc_start: 0.7258 (tp) cc_final: 0.6929 (tp) REVERT: P 310 MET cc_start: 0.3415 (mmt) cc_final: 0.2616 (mmt) REVERT: Q 68 MET cc_start: 0.8032 (tpt) cc_final: 0.7500 (tpt) REVERT: Q 110 MET cc_start: 0.6097 (mmm) cc_final: 0.5820 (mmm) outliers start: 62 outliers final: 40 residues processed: 334 average time/residue: 0.2556 time to fit residues: 143.3341 Evaluate side-chains 317 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 225 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 384 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 203 HIS ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 112 GLN G 115 GLN M 53 GLN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 HIS ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.078875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053383 restraints weight = 160491.745| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.76 r_work: 0.2878 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43328 Z= 0.127 Angle : 0.558 13.873 58689 Z= 0.279 Chirality : 0.042 0.167 6593 Planarity : 0.004 0.055 7406 Dihedral : 9.846 158.405 6165 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 1.54 % Allowed : 9.09 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.20 (0.11), residues: 5164 helix: -0.00 (0.13), residues: 1771 sheet: -1.10 (0.19), residues: 664 loop : -1.22 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 293 TYR 0.017 0.001 TYR D 47 PHE 0.018 0.001 PHE A 462 TRP 0.027 0.001 TRP A 337 HIS 0.008 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00289 (43303) covalent geometry : angle 0.54351 (58653) hydrogen bonds : bond 0.03253 ( 1329) hydrogen bonds : angle 4.52929 ( 3813) metal coordination : bond 0.00668 ( 25) metal coordination : angle 5.15024 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8974 (ptp) cc_final: 0.8694 (ptp) REVERT: A 281 MET cc_start: 0.8889 (mmm) cc_final: 0.8609 (mmp) REVERT: A 646 MET cc_start: 0.9246 (mmm) cc_final: 0.8250 (mmm) REVERT: A 1151 TYR cc_start: 0.8352 (t80) cc_final: 0.7961 (t80) REVERT: A 1228 GLU cc_start: 0.8511 (tt0) cc_final: 0.7698 (tm-30) REVERT: A 1384 PHE cc_start: 0.7243 (m-10) cc_final: 0.6996 (m-80) REVERT: B 526 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9060 (pp) REVERT: C 90 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: D 40 GLN cc_start: 0.8746 (tt0) cc_final: 0.8503 (mp10) REVERT: D 76 HIS cc_start: 0.9200 (OUTLIER) cc_final: 0.8859 (t70) REVERT: E 18 MET cc_start: 0.9179 (mmm) cc_final: 0.8975 (mtm) REVERT: E 54 ARG cc_start: 0.8464 (mmt180) cc_final: 0.8168 (mmp-170) REVERT: E 55 ARG cc_start: 0.8637 (mpt90) cc_final: 0.8394 (tmm160) REVERT: E 72 MET cc_start: 0.8429 (ttp) cc_final: 0.8051 (ttp) REVERT: E 141 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (mp0) REVERT: E 152 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7851 (p) REVERT: F 83 LEU cc_start: 0.9231 (pt) cc_final: 0.8984 (pp) REVERT: G 7 MET cc_start: 0.8473 (mtm) cc_final: 0.8116 (ttm) REVERT: G 9 ASP cc_start: 0.8578 (t0) cc_final: 0.8210 (t70) REVERT: G 120 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: I 3 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8770 (mm) REVERT: I 80 MET cc_start: 0.8209 (tpp) cc_final: 0.7731 (tpp) REVERT: I 91 MET cc_start: 0.5261 (ttp) cc_final: 0.5049 (tpp) REVERT: K 70 TYR cc_start: 0.9620 (p90) cc_final: 0.9398 (p90) REVERT: M 60 MET cc_start: 0.8250 (mtp) cc_final: 0.6782 (mmm) REVERT: M 314 ILE cc_start: 0.3547 (mt) cc_final: 0.3313 (mt) REVERT: M 319 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7264 (tpt) REVERT: M 386 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6589 (mm) REVERT: M 394 ILE cc_start: 0.5555 (OUTLIER) cc_final: 0.5147 (mt) REVERT: N 350 MET cc_start: 0.8717 (tpp) cc_final: 0.8452 (mpp) REVERT: N 398 ARG cc_start: 0.5616 (ttm170) cc_final: 0.4863 (mtp180) REVERT: O 133 MET cc_start: 0.3045 (ptt) cc_final: 0.2768 (ptt) REVERT: O 455 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8187 (ttpt) REVERT: O 531 MET cc_start: 0.7411 (ttt) cc_final: 0.7164 (mtp) REVERT: Q 49 LYS cc_start: 0.5468 (mmtt) cc_final: 0.5242 (mmtt) REVERT: Q 68 MET cc_start: 0.8079 (tpt) cc_final: 0.7485 (tpt) REVERT: Q 110 MET cc_start: 0.6404 (mmm) cc_final: 0.6015 (mmm) outliers start: 71 outliers final: 41 residues processed: 337 average time/residue: 0.2513 time to fit residues: 143.8110 Evaluate side-chains 322 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 320 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 407 optimal weight: 8.9990 chunk 349 optimal weight: 8.9990 chunk 413 optimal weight: 0.0980 chunk 171 optimal weight: 5.9990 chunk 412 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 476 optimal weight: 20.0000 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 HIS ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS O 534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.076722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.051056 restraints weight = 162824.973| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.78 r_work: 0.2804 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 43328 Z= 0.325 Angle : 0.714 18.622 58689 Z= 0.355 Chirality : 0.046 0.194 6593 Planarity : 0.004 0.055 7406 Dihedral : 10.010 157.271 6165 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.46 % Favored : 94.50 % Rotamer: Outliers : 1.87 % Allowed : 9.44 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.17 (0.11), residues: 5164 helix: 0.07 (0.12), residues: 1776 sheet: -1.33 (0.19), residues: 678 loop : -1.17 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 85 TYR 0.037 0.002 TYR B 357 PHE 0.023 0.002 PHE A 462 TRP 0.030 0.002 TRP A 337 HIS 0.015 0.002 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00737 (43303) covalent geometry : angle 0.69569 (58653) hydrogen bonds : bond 0.03958 ( 1329) hydrogen bonds : angle 4.87169 ( 3813) metal coordination : bond 0.01488 ( 25) metal coordination : angle 6.50463 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 268 time to evaluate : 1.680 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 48 HIS cc_start: 0.6805 (p-80) cc_final: 0.6587 (p-80) REVERT: A 116 MET cc_start: 0.6108 (mmm) cc_final: 0.5775 (mmm) REVERT: A 794 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.9034 (mt0) REVERT: A 1151 TYR cc_start: 0.8604 (t80) cc_final: 0.8292 (t80) REVERT: B 526 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9111 (pp) REVERT: C 90 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: D 40 GLN cc_start: 0.8789 (tt0) cc_final: 0.8482 (mp10) REVERT: D 76 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8834 (t70) REVERT: E 18 MET cc_start: 0.9266 (mmm) cc_final: 0.9012 (mtm) REVERT: E 54 ARG cc_start: 0.8441 (mmt180) cc_final: 0.8127 (mmp-170) REVERT: E 56 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.8018 (p) REVERT: E 72 MET cc_start: 0.8656 (ttp) cc_final: 0.7953 (mtp) REVERT: E 141 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8661 (mp0) REVERT: E 152 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7887 (p) REVERT: F 126 THR cc_start: 0.6648 (OUTLIER) cc_final: 0.6414 (p) REVERT: G 7 MET cc_start: 0.8494 (mtm) cc_final: 0.8148 (ttm) REVERT: G 9 ASP cc_start: 0.8729 (t0) cc_final: 0.8327 (t70) REVERT: G 120 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: I 80 MET cc_start: 0.8212 (tpp) cc_final: 0.7676 (tpp) REVERT: L 44 MET cc_start: 0.9412 (mmt) cc_final: 0.8902 (mmm) REVERT: M 270 MET cc_start: 0.8573 (ptm) cc_final: 0.8247 (ppp) REVERT: M 319 MET cc_start: 0.7579 (ttt) cc_final: 0.7212 (tpt) REVERT: M 394 ILE cc_start: 0.5733 (OUTLIER) cc_final: 0.5392 (mp) REVERT: N 398 ARG cc_start: 0.5503 (ttm170) cc_final: 0.4792 (mtp180) REVERT: O 398 MET cc_start: 0.5124 (mmm) cc_final: 0.4778 (ttm) REVERT: O 455 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8245 (ttpt) REVERT: Q 49 LYS cc_start: 0.5391 (mmtt) cc_final: 0.5141 (mmtt) REVERT: Q 68 MET cc_start: 0.8170 (tpt) cc_final: 0.7577 (tpt) REVERT: Q 110 MET cc_start: 0.6443 (mmm) cc_final: 0.6152 (mmm) outliers start: 86 outliers final: 55 residues processed: 340 average time/residue: 0.2338 time to fit residues: 135.9983 Evaluate side-chains 324 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 258 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 15 ASN Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 132 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 263 optimal weight: 0.8980 chunk 389 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 458 optimal weight: 10.0000 chunk 451 optimal weight: 0.4980 chunk 320 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** A1385 HIS B 438 GLN B 692 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN H 130 ASN ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 GLN ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** 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 = 0.3713 r_free = 0.3713 target = 0.078557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052994 restraints weight = 160439.325| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.77 r_work: 0.2864 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43328 Z= 0.119 Angle : 0.569 14.283 58689 Z= 0.282 Chirality : 0.042 0.169 6593 Planarity : 0.004 0.049 7406 Dihedral : 9.827 157.947 6165 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 1.30 % Allowed : 10.57 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.77 (0.12), residues: 5164 helix: 0.43 (0.13), residues: 1776 sheet: -1.07 (0.19), residues: 652 loop : -0.96 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 85 TYR 0.020 0.001 TYR D 47 PHE 0.016 0.001 PHE A 462 TRP 0.022 0.001 TRP A 337 HIS 0.008 0.001 HIS M 420 Details of bonding type rmsd covalent geometry : bond 0.00271 (43303) covalent geometry : angle 0.55335 (58653) hydrogen bonds : bond 0.03127 ( 1329) hydrogen bonds : angle 4.44572 ( 3813) metal coordination : bond 0.00698 ( 25) metal coordination : angle 5.37212 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 273 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9010 (ptp) cc_final: 0.8796 (ptp) REVERT: A 48 HIS cc_start: 0.6837 (p-80) cc_final: 0.6612 (p-80) REVERT: A 116 MET cc_start: 0.6140 (mmm) cc_final: 0.5777 (mmm) REVERT: A 337 TRP cc_start: 0.8125 (t60) cc_final: 0.7895 (t60) REVERT: A 426 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 646 MET cc_start: 0.9259 (mmm) cc_final: 0.8420 (mmm) REVERT: A 1151 TYR cc_start: 0.8442 (t80) cc_final: 0.8042 (t80) REVERT: B 526 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9058 (pp) REVERT: C 90 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: D 40 GLN cc_start: 0.8831 (tt0) cc_final: 0.8505 (mp10) REVERT: D 51 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6571 (pttm) REVERT: D 76 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8802 (t70) REVERT: E 54 ARG cc_start: 0.8324 (mmt180) cc_final: 0.8044 (mmp-170) REVERT: E 56 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7758 (p) REVERT: E 72 MET cc_start: 0.8553 (ttp) cc_final: 0.8128 (ttp) REVERT: E 141 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8584 (mp0) REVERT: E 152 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7742 (p) REVERT: F 126 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6442 (p) REVERT: G 7 MET cc_start: 0.8443 (mtm) cc_final: 0.8078 (ttm) REVERT: G 9 ASP cc_start: 0.8662 (t0) cc_final: 0.8317 (t70) REVERT: G 44 LEU cc_start: 0.8712 (tt) cc_final: 0.8504 (pp) REVERT: G 120 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: I 80 MET cc_start: 0.8327 (tpp) cc_final: 0.7826 (tpp) REVERT: K 70 TYR cc_start: 0.9650 (p90) cc_final: 0.9432 (p90) REVERT: L 44 MET cc_start: 0.9366 (mmt) cc_final: 0.8900 (mmm) REVERT: M 319 MET cc_start: 0.7649 (ttt) cc_final: 0.7259 (tpt) REVERT: M 394 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5476 (mp) REVERT: N 398 ARG cc_start: 0.5437 (ttm170) cc_final: 0.4823 (mtp180) REVERT: O 455 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8177 (ttpt) REVERT: O 531 MET cc_start: 0.7489 (ttt) cc_final: 0.7272 (mtp) REVERT: P 310 MET cc_start: 0.3328 (mmt) cc_final: 0.3105 (tpp) REVERT: Q 49 LYS cc_start: 0.5380 (mmtt) cc_final: 0.5165 (mmtt) REVERT: Q 68 MET cc_start: 0.8145 (tpt) cc_final: 0.7522 (tpt) REVERT: Q 110 MET cc_start: 0.6365 (mmm) cc_final: 0.6016 (mmm) outliers start: 60 outliers final: 38 residues processed: 319 average time/residue: 0.2624 time to fit residues: 141.1531 Evaluate side-chains 313 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 429 LEU Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 64 optimal weight: 0.9990 chunk 373 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 472 optimal weight: 8.9990 chunk 477 optimal weight: 9.9990 chunk 427 optimal weight: 0.0970 chunk 141 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 400 optimal weight: 9.9990 chunk 258 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** 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 = 0.3698 r_free = 0.3698 target = 0.077851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052239 restraints weight = 162107.213| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.78 r_work: 0.2843 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43328 Z= 0.179 Angle : 0.595 14.743 58689 Z= 0.293 Chirality : 0.043 0.172 6593 Planarity : 0.004 0.049 7406 Dihedral : 9.803 157.815 6165 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.47 % Rotamer: Outliers : 1.30 % Allowed : 10.74 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.66 (0.12), residues: 5164 helix: 0.56 (0.13), residues: 1785 sheet: -1.04 (0.19), residues: 647 loop : -0.92 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 62 TYR 0.020 0.001 TYR B 357 PHE 0.036 0.001 PHE A 462 TRP 0.020 0.001 TRP A 337 HIS 0.012 0.001 HIS M 44 Details of bonding type rmsd covalent geometry : bond 0.00413 (43303) covalent geometry : angle 0.57980 (58653) hydrogen bonds : bond 0.03220 ( 1329) hydrogen bonds : angle 4.45807 ( 3813) metal coordination : bond 0.00923 ( 25) metal coordination : angle 5.39307 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 1.714 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 22 MET cc_start: 0.9052 (ptp) cc_final: 0.8843 (ptp) REVERT: A 116 MET cc_start: 0.6279 (mmm) cc_final: 0.5939 (mmm) REVERT: A 337 TRP cc_start: 0.8148 (t60) cc_final: 0.7903 (t60) REVERT: A 646 MET cc_start: 0.9270 (mmm) cc_final: 0.8922 (mmt) REVERT: A 1151 TYR cc_start: 0.8563 (t80) cc_final: 0.8214 (t80) REVERT: B 415 MET cc_start: 0.9004 (mmt) cc_final: 0.8781 (mmt) REVERT: B 526 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9074 (pp) REVERT: B 641 CYS cc_start: 0.9316 (m) cc_final: 0.9072 (p) REVERT: C 90 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: D 40 GLN cc_start: 0.8808 (tt0) cc_final: 0.8479 (mp10) REVERT: D 76 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8810 (t70) REVERT: E 18 MET cc_start: 0.9253 (mmm) cc_final: 0.8989 (mtm) REVERT: E 56 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7813 (p) REVERT: E 72 MET cc_start: 0.8599 (ttp) cc_final: 0.8185 (ttp) REVERT: E 141 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8613 (mp0) REVERT: E 152 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7761 (p) REVERT: F 126 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6277 (p) REVERT: G 7 MET cc_start: 0.8413 (mtm) cc_final: 0.8054 (ttm) REVERT: G 9 ASP cc_start: 0.8686 (t0) cc_final: 0.8348 (t70) REVERT: G 120 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: I 80 MET cc_start: 0.8333 (tpp) cc_final: 0.7872 (tpp) REVERT: L 44 MET cc_start: 0.9359 (mmt) cc_final: 0.8853 (mmm) REVERT: M 60 MET cc_start: 0.8794 (tpp) cc_final: 0.8136 (mmm) REVERT: M 319 MET cc_start: 0.7446 (ttt) cc_final: 0.7201 (tpt) REVERT: M 357 MET cc_start: 0.8619 (tmm) cc_final: 0.8410 (tmm) REVERT: M 394 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5495 (mp) REVERT: N 398 ARG cc_start: 0.5378 (ttm170) cc_final: 0.4630 (mtp180) REVERT: O 394 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.6062 (mmp) REVERT: O 398 MET cc_start: 0.5614 (tpp) cc_final: 0.4670 (ttm) REVERT: O 455 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8208 (ttpt) REVERT: Q 49 LYS cc_start: 0.5392 (mmtt) cc_final: 0.5110 (mmtm) REVERT: Q 68 MET cc_start: 0.8161 (tpt) cc_final: 0.7615 (tpt) REVERT: Q 82 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7486 (tm-30) REVERT: Q 92 MET cc_start: 0.7060 (ptp) cc_final: 0.6599 (ptp) REVERT: Q 110 MET cc_start: 0.6583 (mmm) cc_final: 0.6224 (mmm) REVERT: Q 111 MET cc_start: 0.8152 (mmm) cc_final: 0.7937 (mmp) outliers start: 60 outliers final: 41 residues processed: 308 average time/residue: 0.2328 time to fit residues: 122.4307 Evaluate side-chains 305 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1062 MET Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 429 LEU Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 156 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 456 optimal weight: 9.9990 chunk 186 optimal weight: 0.0370 chunk 247 optimal weight: 3.9990 chunk 437 optimal weight: 3.9990 chunk 475 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- 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** ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.077806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052252 restraints weight = 160676.526| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.75 r_work: 0.2845 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43328 Z= 0.177 Angle : 0.599 14.464 58689 Z= 0.296 Chirality : 0.043 0.173 6593 Planarity : 0.004 0.051 7406 Dihedral : 9.788 157.662 6165 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 1.35 % Allowed : 10.91 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.58 (0.12), residues: 5164 helix: 0.64 (0.13), residues: 1783 sheet: -0.96 (0.19), residues: 641 loop : -0.89 (0.12), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.019 0.001 TYR B 357 PHE 0.032 0.001 PHE A 462 TRP 0.019 0.001 TRP A 337 HIS 0.009 0.001 HIS M 420 Details of bonding type rmsd covalent geometry : bond 0.00407 (43303) covalent geometry : angle 0.58412 (58653) hydrogen bonds : bond 0.03181 ( 1329) hydrogen bonds : angle 4.44208 ( 3813) metal coordination : bond 0.00927 ( 25) metal coordination : angle 5.46147 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 2.097 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: A 48 HIS cc_start: 0.7635 (p-80) cc_final: 0.7406 (p-80) REVERT: A 116 MET cc_start: 0.6185 (mmm) cc_final: 0.5857 (mmm) REVERT: A 281 MET cc_start: 0.9018 (mmm) cc_final: 0.8272 (ptt) REVERT: A 646 MET cc_start: 0.9278 (mmm) cc_final: 0.8921 (mmt) REVERT: A 1151 TYR cc_start: 0.8586 (t80) cc_final: 0.8213 (t80) REVERT: B 415 MET cc_start: 0.9009 (mmt) cc_final: 0.8809 (mmt) REVERT: B 526 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9068 (pp) REVERT: B 641 CYS cc_start: 0.9342 (m) cc_final: 0.9055 (p) REVERT: C 90 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: D 40 GLN cc_start: 0.8811 (tt0) cc_final: 0.8489 (mp10) REVERT: D 76 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8818 (t70) REVERT: E 18 MET cc_start: 0.9262 (mmm) cc_final: 0.8986 (mtm) REVERT: E 56 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7780 (p) REVERT: E 72 MET cc_start: 0.8609 (ttp) cc_final: 0.8182 (ttp) REVERT: E 141 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8600 (mp0) REVERT: E 152 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7745 (p) REVERT: F 126 THR cc_start: 0.6530 (OUTLIER) cc_final: 0.6288 (p) REVERT: G 7 MET cc_start: 0.8435 (mtm) cc_final: 0.8069 (ttm) REVERT: G 9 ASP cc_start: 0.8699 (t0) cc_final: 0.8349 (t70) REVERT: G 120 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: I 80 MET cc_start: 0.8338 (tpp) cc_final: 0.7892 (tpp) REVERT: I 85 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.7519 (mtm110) REVERT: L 44 MET cc_start: 0.9347 (mmt) cc_final: 0.8850 (mmm) REVERT: M 60 MET cc_start: 0.8830 (tpp) cc_final: 0.8187 (mmm) REVERT: M 319 MET cc_start: 0.7520 (ttt) cc_final: 0.7270 (tpt) REVERT: M 357 MET cc_start: 0.8633 (tmm) cc_final: 0.8426 (tmm) REVERT: M 394 ILE cc_start: 0.5766 (OUTLIER) cc_final: 0.5474 (mp) REVERT: N 398 ARG cc_start: 0.5357 (ttm170) cc_final: 0.4751 (mtp180) REVERT: O 394 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5970 (mmp) REVERT: O 398 MET cc_start: 0.5559 (tpp) cc_final: 0.4676 (ttm) REVERT: O 455 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8209 (ttpt) REVERT: P 207 ASN cc_start: 0.7783 (t0) cc_final: 0.7433 (p0) REVERT: Q 49 LYS cc_start: 0.5246 (mmtt) cc_final: 0.4970 (mmtm) REVERT: Q 68 MET cc_start: 0.8183 (tpt) cc_final: 0.7653 (tpt) REVERT: Q 82 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7426 (tm-30) REVERT: Q 92 MET cc_start: 0.7060 (ptp) cc_final: 0.6603 (ptp) REVERT: Q 110 MET cc_start: 0.6595 (mmm) cc_final: 0.6165 (mmm) outliers start: 62 outliers final: 43 residues processed: 309 average time/residue: 0.2479 time to fit residues: 130.3687 Evaluate side-chains 308 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1062 MET Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 429 LEU Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 167 optimal weight: 5.9990 chunk 400 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 326 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 369 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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** ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** 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 = 0.3689 r_free = 0.3689 target = 0.077393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051863 restraints weight = 161888.957| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.76 r_work: 0.2834 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 43328 Z= 0.201 Angle : 0.625 16.023 58689 Z= 0.306 Chirality : 0.043 0.180 6593 Planarity : 0.004 0.051 7406 Dihedral : 9.803 157.116 6165 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.14 % Rotamer: Outliers : 1.22 % Allowed : 11.09 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.12), residues: 5164 helix: 0.68 (0.13), residues: 1783 sheet: -1.04 (0.19), residues: 657 loop : -0.88 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 364 TYR 0.021 0.001 TYR B 357 PHE 0.032 0.001 PHE A 462 TRP 0.026 0.001 TRP A 337 HIS 0.012 0.001 HIS M 420 Details of bonding type rmsd covalent geometry : bond 0.00462 (43303) covalent geometry : angle 0.60735 (58653) hydrogen bonds : bond 0.03253 ( 1329) hydrogen bonds : angle 4.49901 ( 3813) metal coordination : bond 0.01053 ( 25) metal coordination : angle 5.94952 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10328 Ramachandran restraints generated. 5164 Oldfield, 0 Emsley, 5164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 259 time to evaluate : 1.745 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 48 HIS cc_start: 0.7544 (p-80) cc_final: 0.7323 (p-80) REVERT: A 116 MET cc_start: 0.6076 (mmm) cc_final: 0.5787 (mmm) REVERT: A 281 MET cc_start: 0.9061 (mmm) cc_final: 0.8358 (ptt) REVERT: A 646 MET cc_start: 0.9277 (mmm) cc_final: 0.8905 (mmt) REVERT: A 1151 TYR cc_start: 0.8614 (t80) cc_final: 0.8219 (t80) REVERT: B 526 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9065 (pp) REVERT: C 90 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: D 40 GLN cc_start: 0.8812 (tt0) cc_final: 0.8492 (mp10) REVERT: D 76 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8813 (t70) REVERT: E 18 MET cc_start: 0.9269 (mmm) cc_final: 0.8989 (mtm) REVERT: E 56 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7829 (p) REVERT: E 72 MET cc_start: 0.8637 (ttp) cc_final: 0.8213 (ttp) REVERT: E 141 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8605 (mp0) REVERT: E 152 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7760 (p) REVERT: F 126 THR cc_start: 0.6516 (OUTLIER) cc_final: 0.6272 (p) REVERT: G 7 MET cc_start: 0.8435 (mtm) cc_final: 0.8063 (ttm) REVERT: G 9 ASP cc_start: 0.8722 (t0) cc_final: 0.8377 (t70) REVERT: G 120 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: I 85 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.7292 (mtm110) REVERT: I 91 MET cc_start: 0.5274 (ttp) cc_final: 0.5000 (tpp) REVERT: M 60 MET cc_start: 0.8912 (tpp) cc_final: 0.8441 (mmm) REVERT: M 319 MET cc_start: 0.7570 (ttt) cc_final: 0.7297 (tpt) REVERT: M 357 MET cc_start: 0.8630 (tmm) cc_final: 0.8417 (tmm) REVERT: M 394 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5505 (mp) REVERT: N 398 ARG cc_start: 0.5340 (ttm170) cc_final: 0.4645 (mtp180) REVERT: O 394 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5974 (mmp) REVERT: O 398 MET cc_start: 0.5651 (tpp) cc_final: 0.4724 (ttm) REVERT: O 434 MET cc_start: 0.8653 (ppp) cc_final: 0.8433 (ppp) REVERT: O 455 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8307 (ttpt) REVERT: P 207 ASN cc_start: 0.7784 (t0) cc_final: 0.7361 (p0) REVERT: Q 68 MET cc_start: 0.8231 (tpt) cc_final: 0.7771 (tpt) REVERT: Q 82 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7342 (tm-30) REVERT: Q 92 MET cc_start: 0.7063 (ptp) cc_final: 0.6633 (ptp) REVERT: Q 111 MET cc_start: 0.8116 (mmm) cc_final: 0.4500 (ptt) outliers start: 56 outliers final: 42 residues processed: 303 average time/residue: 0.2465 time to fit residues: 126.9118 Evaluate side-chains 304 residues out of total 4609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 1062 MET Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain M residue 394 ILE Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 429 LEU Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 349 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 478 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 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 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.077362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051834 restraints weight = 162260.460| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.76 r_work: 0.2833 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.273 43328 Z= 0.238 Angle : 0.705 59.197 58689 Z= 0.364 Chirality : 0.044 0.557 6593 Planarity : 0.004 0.051 7406 Dihedral : 9.800 157.112 6165 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 1.24 % Allowed : 11.24 % Favored : 87.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.12), residues: 5164 helix: 0.69 (0.13), residues: 1783 sheet: -1.04 (0.19), residues: 657 loop : -0.88 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 104 TYR 0.019 0.001 TYR B 357 PHE 0.030 0.001 PHE A 462 TRP 0.023 0.001 TRP A 337 HIS 0.051 0.001 HIS M 420 Details of bonding type rmsd covalent geometry : bond 0.00544 (43303) covalent geometry : angle 0.68953 (58653) hydrogen bonds : bond 0.03273 ( 1329) hydrogen bonds : angle 4.49861 ( 3813) metal coordination : bond 0.01084 ( 25) metal coordination : angle 5.94270 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10880.37 seconds wall clock time: 187 minutes 33.25 seconds (11253.25 seconds total)