Starting phenix.real_space_refine on Tue Sep 15 12:53:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fji_31621/09_2026/7fji_31621.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 43 5.49 5 S 266 5.16 5 C 24861 2.51 5 N 6869 2.21 5 O 7486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39536 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1367, 10732 Classifications: {'peptide': 1367} Link IDs: {'PTRANS': 64, 'TRANS': 1302} 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: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} 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: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 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: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} 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: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1682 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3546 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "Q" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 724 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNAv2': 4} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Chain: "X" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "Y" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 90.635 42.831 66.130 1.00 82.01 S ATOM 565 SG CYS A 72 88.961 44.401 62.455 1.00 78.11 S ATOM 613 SG CYS A 79 90.861 46.764 64.793 1.00 76.28 S ATOM 854 SG CYS A 109 56.021 60.607 96.075 1.00 89.23 S ATOM 876 SG CYS A 112 53.647 58.670 93.339 1.00 92.78 S ATOM 1271 SG CYS A 159 52.728 59.452 96.799 1.00102.77 S ATOM 18999 SG CYS B1080 73.707 52.371 61.720 1.00 70.89 S ATOM 19018 SG CYS B1083 73.783 52.844 65.621 1.00 70.04 S ATOM 19084 SG CYS B1092 75.455 49.728 64.169 1.00 74.21 S ATOM 19112 SG CYS B1095 71.545 50.014 64.202 1.00 73.49 S ATOM 28022 SG CYS I 5 86.350 91.981 144.689 1.00114.52 S ATOM 28039 SG CYS I 8 86.844 88.147 143.079 1.00114.88 S ATOM 28169 SG CYS I 25 83.722 89.431 141.903 1.00122.98 S ATOM 28190 SG CYS I 28 84.070 89.414 145.594 1.00124.29 S ATOM 28884 SG CYS J 7 147.824 87.925 64.824 1.00 54.01 S ATOM 28908 SG CYS J 10 147.477 90.855 63.059 1.00 57.92 S ATOM 29172 SG CYS J 44 148.226 92.064 64.527 1.00 57.10 S ATOM 29178 SG CYS J 45 151.321 90.191 64.711 1.00 54.89 S ATOM 30221 SG CYS L 19 147.081 48.045 83.240 1.00 81.26 S ATOM 30383 SG CYS L 39 146.554 47.002 87.328 1.00 97.98 S ATOM 37698 SG CYS P 287 59.463 36.050 82.038 1.00121.28 S Time building chain proxies: 8.76, per 1000 atoms: 0.22 Number of scatterers: 39536 At special positions: 0 Unit cell: (183.396, 155.992, 178.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 266 16.00 P 43 15.00 O 7486 8.00 N 6869 7.00 C 24861 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 18 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9154 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 49 sheets defined 40.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.786A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.502A pdb=" N GLY A 61 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.674A pdb=" N GLY A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.917A 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 250 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 278 through 300 Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.911A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.716A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.823A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 546 through 553 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.921A pdb=" N ASP A 576 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 4.229A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 662 through 672 Processing helix chain 'A' and resid 672 through 695 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 706 through 733 removed outlier: 3.635A pdb=" N TYR A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 771 removed outlier: 3.599A pdb=" N CYS A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 828 through 832 removed outlier: 3.926A pdb=" N GLY A 832 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.879A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.528A 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 954 Processing helix chain 'A' and resid 955 through 961 removed outlier: 3.623A pdb=" N CYS A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 988 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1024 Processing helix chain 'A' and resid 1032 through 1048 Proline residue: A1044 - end of helix removed outlier: 3.772A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.700A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.720A pdb=" N ALA A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1100 " --> pdb=" O ASP A1096 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1145 through 1153 removed outlier: 4.008A pdb=" N TYR A1151 " --> pdb=" O GLU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 4.117A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 removed outlier: 3.611A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.877A pdb=" N THR A1246 " --> pdb=" O GLY A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 Processing helix chain 'A' and resid 1259 through 1278 removed outlier: 3.515A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 removed outlier: 4.065A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1319 Processing helix chain 'A' and resid 1323 through 1335 removed outlier: 3.980A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1350 Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 3.697A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.634A 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 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 35 Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.578A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.630A pdb=" N CYS B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.624A pdb=" N ALA B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 273 Proline residue: B 267 - end of helix removed outlier: 3.610A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.912A pdb=" N LEU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 347 removed outlier: 3.868A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.908A pdb=" N LEU B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 5.652A pdb=" N ARG B 407 " --> pdb=" O LYS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 427 through 430 removed outlier: 3.540A pdb=" N LYS B 430 " --> pdb=" O LYS B 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 444 through 452 removed outlier: 3.539A pdb=" N ALA B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 516 removed outlier: 4.174A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.615A pdb=" N LEU B 526 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.554A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.907A pdb=" N ASN B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 3.939A pdb=" N GLU B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 759 through 765 Processing helix chain 'B' and resid 803 through 807 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.661A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 954 removed outlier: 3.764A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.887A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1019 Processing helix chain 'B' and resid 1048 through 1058 removed outlier: 3.528A pdb=" N ASP B1053 " --> pdb=" O GLU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 removed outlier: 4.184A pdb=" N GLN B1118 " --> pdb=" O PHE B1114 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.961A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 290 through 295 removed outlier: 4.319A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 28 removed outlier: 3.526A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.862A pdb=" N SER D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.608A pdb=" N THR D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 77 removed outlier: 4.138A pdb=" N VAL D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.761A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.683A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 51 through 56 removed outlier: 4.242A pdb=" N THR E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.911A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.896A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 removed outlier: 4.001A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.752A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.619A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.790A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 48 through 60 removed outlier: 3.577A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 126 Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.608A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 154 removed outlier: 3.599A pdb=" N ASP M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 201 Processing helix chain 'M' and resid 215 through 222 removed outlier: 3.618A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 226 Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.861A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 257 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 388 through 396 removed outlier: 3.639A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 removed outlier: 3.525A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 32 Processing helix chain 'O' and resid 35 through 43 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 78 through 83 removed outlier: 4.120A pdb=" N VAL O 82 " --> pdb=" O GLN O 78 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 78 through 83' Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 87 through 99 removed outlier: 3.542A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 113 Processing helix chain 'O' and resid 118 through 133 removed outlier: 4.283A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 154 removed outlier: 3.573A pdb=" N VAL O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 152 " --> pdb=" O PHE O 148 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR O 154 " --> pdb=" O ARG O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 257 removed outlier: 3.710A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 273 removed outlier: 3.600A pdb=" N SER O 264 " --> pdb=" O ASP O 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 296 removed outlier: 3.601A pdb=" N ILE O 293 " --> pdb=" O SER O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 317 removed outlier: 3.538A pdb=" N ASP O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 358 removed outlier: 3.678A pdb=" N LEU O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 367 removed outlier: 3.733A pdb=" N CYS O 362 " --> pdb=" O PHE O 358 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 379 through 384 removed outlier: 3.811A pdb=" N ALA O 384 " --> pdb=" O VAL O 380 " (cutoff:3.500A) Processing helix chain 'O' and resid 387 through 401 removed outlier: 3.653A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 429 through 453 removed outlier: 3.621A pdb=" N LEU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG O 449 " --> pdb=" O ASN O 445 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 456 No H-bonds generated for 'chain 'O' and resid 454 through 456' Processing helix chain 'O' and resid 457 through 465 removed outlier: 3.753A pdb=" N LEU O 461 " --> pdb=" O ASN O 457 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU O 462 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS O 463 " --> pdb=" O ARG O 459 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER O 464 " --> pdb=" O LEU O 460 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN O 465 " --> pdb=" O LEU O 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 457 through 465' Processing helix chain 'O' and resid 492 through 516 removed outlier: 3.653A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL O 516 " --> pdb=" O SER O 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 530 removed outlier: 3.984A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 206 removed outlier: 3.937A pdb=" N GLN P 205 " --> pdb=" O ASN P 201 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG P 206 " --> pdb=" O PRO P 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 201 through 206' Processing helix chain 'P' and resid 219 through 228 removed outlier: 3.569A pdb=" N VAL P 228 " --> pdb=" O GLY P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 246 Processing helix chain 'P' and resid 246 through 254 removed outlier: 3.532A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA P 254 " --> pdb=" O MET P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.701A pdb=" N LEU P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS P 290 " --> pdb=" O PRO P 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 285 through 290' Processing helix chain 'P' and resid 291 through 295 Processing helix chain 'P' and resid 303 through 306 Processing helix chain 'P' and resid 307 through 314 removed outlier: 3.760A pdb=" N THR P 311 " --> pdb=" O CYS P 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 62 removed outlier: 4.102A pdb=" N THR Q 50 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 77 removed outlier: 3.864A pdb=" N PHE Q 74 " --> pdb=" O ARG Q 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 7.317A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL G 8 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL D 3 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 5 removed outlier: 7.317A pdb=" N GLU A 4 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 4.622A pdb=" N ILE A 15 " --> pdb=" O SER B1129 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SER B1129 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.766A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.926A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 359 through 361 removed outlier: 3.692A pdb=" N LEU B1045 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 3.885A pdb=" N PHE A 488 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.041A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 616 through 620 removed outlier: 6.457A 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: 3.519A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1247 through 1248 removed outlier: 3.832A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU I 53 " --> pdb=" O ALA A1210 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE A1212 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 7.439A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1165 through 1169 removed outlier: 3.861A pdb=" N HIS A1168 " --> pdb=" O VAL A1172 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1172 " --> pdb=" O HIS A1168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A1119 " --> pdb=" O ASN I 40 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN I 40 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A1121 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL I 38 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 66 removed outlier: 7.033A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.748A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'B' and resid 360 through 363 removed outlier: 3.609A pdb=" N ILE B 180 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.805A pdb=" N THR B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 424 through 426 removed outlier: 4.332A pdb=" N ARG B 433 " --> pdb=" O TRP B 424 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC5, first strand: chain 'B' and resid 603 through 604 Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 549 removed outlier: 6.550A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 537 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.802A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.802A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR B 888 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N SER B 864 " --> pdb=" O THR B 888 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 720 through 721 Processing sheet with id=AD1, first strand: chain 'B' and resid 986 through 987 removed outlier: 6.646A pdb=" N LEU B 755 " --> pdb=" O LEU B 909 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL B 911 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 757 " --> pdb=" O VAL B 911 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 927 " --> pdb=" O ASN B 738 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR B 740 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET B 929 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 742 " --> pdb=" O MET B 929 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.246A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.521A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 21 through 22 removed outlier: 4.619A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 230 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 57 removed outlier: 5.944A pdb=" N VAL C 51 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL C 66 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL C 53 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP C 64 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.173A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AD9, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AE1, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE2, first strand: chain 'E' and resid 62 through 63 removed outlier: 5.713A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.574A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.824A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 83 through 87 removed outlier: 4.796A pdb=" N GLU G 83 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE G 150 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.737A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AE9, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.558A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP I 106 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AF2, first strand: chain 'N' and resid 370 through 387 removed outlier: 6.809A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU N 357 " --> pdb=" O TYR M 30 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE N 356 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LYS N 380 " --> pdb=" O PHE N 356 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU N 266 " --> pdb=" O HIS N 381 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.674A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 116 through 117 1585 hydrogen bonds defined for protein. 4395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.24 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 15049 1.38 - 1.57: 24798 1.57 - 1.76: 86 1.76 - 1.95: 406 1.95 - 2.14: 12 Bond restraints: 40351 Sorted by residual: bond pdb=" CA TYR A1187 " pdb=" C TYR A1187 " ideal model delta sigma weight residual 1.523 1.597 -0.074 1.34e-02 5.57e+03 3.05e+01 bond pdb=" C1' DT X 35 " pdb=" N1 DT X 35 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.96e+01 bond pdb=" CA SER A 776 " pdb=" CB SER A 776 " ideal model delta sigma weight residual 1.533 1.458 0.075 1.39e-02 5.18e+03 2.92e+01 bond pdb=" C1' DT Y 11 " pdb=" N1 DT Y 11 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.83e+01 bond pdb=" C1' DC X 41 " pdb=" N1 DC X 41 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.82e+01 ... (remaining 40346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 53265 3.37 - 6.74: 1268 6.74 - 10.10: 92 10.10 - 13.47: 9 13.47 - 16.84: 24 Bond angle restraints: 54658 Sorted by residual: angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.54 -16.84 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.53 -16.83 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.47 -16.77 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.46 -16.76 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE1 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE2 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.05 -16.35 1.50e+00 4.44e-01 1.19e+02 ... (remaining 54653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.15: 23625 28.15 - 56.30: 964 56.30 - 84.45: 95 84.45 - 112.59: 3 112.59 - 140.74: 2 Dihedral angle restraints: 24689 sinusoidal: 10532 harmonic: 14157 Sorted by residual: dihedral pdb=" C4' G R 8 " pdb=" C3' G R 8 " pdb=" C2' G R 8 " pdb=" C1' G R 8 " ideal model delta sinusoidal sigma weight residual 36.34 1.07 35.28 1 3.10e+00 1.04e-01 1.83e+02 dihedral pdb=" O4' G R 8 " pdb=" C2' G R 8 " pdb=" C1' G R 8 " pdb=" C3' G R 8 " ideal model delta sinusoidal sigma weight residual 25.59 -9.51 35.11 3 3.80e+00 6.93e-02 9.34e+01 dihedral pdb=" O4' G R 8 " pdb=" C4' G R 8 " pdb=" C3' G R 8 " pdb=" C2' G R 8 " ideal model delta sinusoidal sigma weight residual -35.15 -10.92 -24.23 1 4.00e+00 6.25e-02 5.29e+01 ... (remaining 24686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 5672 0.164 - 0.329: 448 0.329 - 0.493: 28 0.493 - 0.657: 4 0.657 - 0.822: 4 Chirality restraints: 6156 Sorted by residual: chirality pdb="FE4 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.73 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb="FE1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.74 0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 6153 not shown) Planarity restraints: 6895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 843 " 0.022 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C THR A 843 " -0.081 2.00e-02 2.50e+03 pdb=" O THR A 843 " 0.032 2.00e-02 2.50e+03 pdb=" N PRO A 844 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 684 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ALA A 684 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA A 684 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG A 685 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 39 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLN D 39 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN D 39 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN D 40 " -0.022 2.00e-02 2.50e+03 ... (remaining 6892 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 16 2.07 - 2.78: 7152 2.78 - 3.48: 53939 3.48 - 4.19: 93177 4.19 - 4.90: 162991 Nonbonded interactions: 317275 Sorted by model distance: nonbonded pdb=" CD GLU A1216 " pdb=" CB ALA I 56 " model vdw 1.362 3.690 nonbonded pdb=" CD2 PHE A1053 " pdb=" CE MET I 80 " model vdw 1.383 3.760 nonbonded pdb=" OE1 GLU A1216 " pdb=" CB ALA I 56 " model vdw 1.389 3.460 nonbonded pdb=" CG PHE A1053 " pdb=" CE MET I 80 " model vdw 1.601 3.680 nonbonded pdb=" OH TYR A 97 " pdb=" O ASN B1121 " model vdw 1.648 3.040 ... (remaining 317270 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 50.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 0.936 40373 Z= 0.617 Angle : 1.424 56.793 54682 Z= 0.903 Chirality : 0.095 0.822 6156 Planarity : 0.007 0.074 6895 Dihedral : 14.496 140.743 15535 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.54 % Favored : 95.30 % Rotamer: Outliers : 3.59 % Allowed : 8.51 % Favored : 87.90 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.12), residues: 4805 helix: -0.64 (0.13), residues: 1688 sheet: 0.01 (0.20), residues: 626 loop : -1.11 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG B 222 TYR 0.057 0.003 TYR B 357 PHE 0.046 0.003 PHE A 462 TRP 0.025 0.003 TRP P 217 HIS 0.014 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.01001 / 0.59 (40351) covalent geometry : angle 1.33894 / 0.90 (54658) hydrogen bonds : bond 0.24295 / 16.14 ( 1559) hydrogen bonds : angle 8.41403 / 5.99 ( 4395) metal coordination : bond 0.23847 / 18.21 ( 22) metal coordination : angle 23.21905 / 11.87 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1222 time to evaluate : 1.569 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: 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 294 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8510 (pttp) REVERT: A 887 ASP cc_start: 0.6978 (p0) cc_final: 0.6698 (p0) REVERT: A 952 ILE cc_start: 0.8866 (mm) cc_final: 0.8627 (mt) REVERT: A 1131 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7884 (ttmt) REVERT: B 424 TRP cc_start: 0.6833 (m100) cc_final: 0.6454 (m100) REVERT: C 34 SER cc_start: 0.7260 (OUTLIER) cc_final: 0.6978 (p) REVERT: C 212 MET cc_start: 0.7909 (mtm) cc_final: 0.7704 (mtm) REVERT: C 319 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7496 (p0) REVERT: D 43 ASN cc_start: 0.5964 (OUTLIER) cc_final: 0.5020 (m-40) REVERT: D 59 ARG cc_start: 0.4777 (OUTLIER) cc_final: 0.3980 (mpp80) REVERT: D 112 GLN cc_start: 0.3265 (tp40) cc_final: 0.3008 (tp40) REVERT: E 139 ILE cc_start: 0.8954 (pt) cc_final: 0.8698 (mt) REVERT: F 125 ILE cc_start: 0.8809 (pt) cc_final: 0.8379 (mt) REVERT: G 71 HIS cc_start: 0.8276 (m-70) cc_final: 0.7663 (m-70) REVERT: G 104 PHE cc_start: 0.6327 (t80) cc_final: 0.6100 (t80) REVERT: H 37 MET cc_start: 0.7423 (mmm) cc_final: 0.6794 (mmp) REVERT: I 2 LEU cc_start: 0.8182 (mt) cc_final: 0.7652 (mm) REVERT: I 47 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8214 (tptt) REVERT: I 74 HIS cc_start: 0.7101 (m-70) cc_final: 0.6877 (m90) REVERT: K 60 MET cc_start: 0.7464 (tpp) cc_final: 0.7154 (tpt) REVERT: N 249 VAL cc_start: 0.7697 (p) cc_final: 0.7019 (m) REVERT: N 331 ILE cc_start: 0.7707 (mt) cc_final: 0.7385 (mm) REVERT: O 414 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: P 203 MET cc_start: 0.7643 (mpp) cc_final: 0.6646 (mpp) REVERT: P 217 TRP cc_start: 0.4187 (t-100) cc_final: 0.3320 (m-10) REVERT: Q 31 VAL cc_start: 0.3890 (OUTLIER) cc_final: 0.3488 (t) REVERT: Q 79 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5848 (tm-30) REVERT: Q 109 GLU cc_start: 0.2951 (tp30) cc_final: 0.2713 (tm-30) outliers start: 154 outliers final: 31 residues processed: 1322 average time/residue: 0.2665 time to fit residues: 553.3735 Evaluate side-chains 595 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 555 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1131 LYS Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain N residue 393 LEU Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 86 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.0980 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 176 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN A 476 HIS A 616 ASN A 693 ASN A 737 GLN A 738 GLN A 836 ASN A 872 GLN A 885 GLN A 927 ASN A 943 ASN A 967 GLN A1180 ASN B 183 GLN B 215 ASN B 320 HIS B 346 GLN B 472 GLN B 616 GLN B 677 HIS B 683 ASN B 823 ASN B 903 GLN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 HIS C 48 ASN C 139 GLN C 206 GLN D 13 ASN D 40 GLN D 98 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN E 210 GLN G 23 ASN G 41 ASN H 46 GLN H 76 ASN I 26 ASN I 74 HIS K 85 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 HIS N 314 ASN O 49 GLN O 113 ASN O 244 GLN O 337 ASN O 377 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS O 445 ASN O 457 ASN O 507 ASN P 274 ASN Q 62 GLN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.095154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071766 restraints weight = 130542.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074459 restraints weight = 60887.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076202 restraints weight = 37244.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.077324 restraints weight = 27122.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078008 restraints weight = 22177.128| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40373 Z= 0.182 Angle : 0.870 49.137 54682 Z= 0.427 Chirality : 0.049 0.334 6156 Planarity : 0.006 0.073 6895 Dihedral : 11.668 149.117 5820 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.66 % Allowed : 15.03 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.11), residues: 4805 helix: -0.25 (0.12), residues: 1717 sheet: 0.16 (0.20), residues: 612 loop : -1.05 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 120 TYR 0.024 0.002 TYR D 52 PHE 0.021 0.002 PHE B 223 TRP 0.050 0.002 TRP G 129 HIS 0.011 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (40351) covalent geometry : angle 0.80266 / 0.42 (54658) hydrogen bonds : bond 0.06188 / 4.14 ( 1559) hydrogen bonds : angle 5.71531 / 4.06 ( 4395) metal coordination : bond 0.01256 / 0.91 ( 22) metal coordination : angle 16.04223 / 7.96 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 676 time to evaluate : 1.396 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8618 (tpp) cc_final: 0.8388 (mmp) REVERT: A 240 MET cc_start: 0.8116 (mtp) cc_final: 0.7597 (mtm) REVERT: A 440 MET cc_start: 0.8163 (mtt) cc_final: 0.7834 (mtm) REVERT: A 577 GLU cc_start: 0.7243 (mt-10) cc_final: 0.7025 (mt-10) REVERT: A 650 MET cc_start: 0.9072 (mmm) cc_final: 0.8851 (mmm) REVERT: A 743 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8327 (t) REVERT: A 746 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 912 MET cc_start: 0.7850 (mmm) cc_final: 0.7521 (mmp) REVERT: A 970 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (mtmm) REVERT: A 1131 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8551 (ttmt) REVERT: A 1236 MET cc_start: 0.8397 (mtp) cc_final: 0.8185 (mtm) REVERT: B 59 MET cc_start: 0.8275 (ppp) cc_final: 0.8016 (ppp) REVERT: B 243 MET cc_start: 0.8894 (mmm) cc_final: 0.8671 (mmm) REVERT: B 379 LYS cc_start: 0.8382 (mttm) cc_final: 0.7891 (mttm) REVERT: B 449 LEU cc_start: 0.9037 (tp) cc_final: 0.8832 (tt) REVERT: B 733 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9154 (pp) REVERT: B 832 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7759 (ttt) REVERT: C 34 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7524 (p) REVERT: C 91 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8164 (ttpp) REVERT: C 141 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7775 (ttm-80) REVERT: D 4 LYS cc_start: 0.8331 (ptmm) cc_final: 0.8088 (ptmm) REVERT: D 59 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6926 (mpp80) REVERT: D 89 HIS cc_start: 0.7345 (t70) cc_final: 0.6984 (t70) REVERT: D 112 GLN cc_start: 0.6530 (tp40) cc_final: 0.6221 (tm-30) REVERT: E 151 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7001 (ttm) REVERT: E 152 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.8010 (m) REVERT: F 57 MET cc_start: 0.8559 (tmm) cc_final: 0.8295 (tmm) REVERT: F 61 GLU cc_start: 0.8605 (mt-10) cc_final: 0.7993 (mt-10) REVERT: F 86 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8285 (mm-30) REVERT: F 100 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7776 (mmt90) REVERT: F 125 ILE cc_start: 0.8895 (pt) cc_final: 0.8522 (pt) REVERT: G 6 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: G 7 MET cc_start: 0.7899 (mtp) cc_final: 0.7529 (mtp) REVERT: G 73 ARG cc_start: 0.8396 (mtm110) cc_final: 0.7847 (mtm110) REVERT: G 184 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.7019 (t80) REVERT: G 185 THR cc_start: 0.8844 (p) cc_final: 0.8621 (p) REVERT: H 37 MET cc_start: 0.8087 (mmm) cc_final: 0.7137 (mmp) REVERT: H 146 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8362 (ttpt) REVERT: I 3 LEU cc_start: 0.8761 (mt) cc_final: 0.8473 (mt) REVERT: I 74 HIS cc_start: 0.6674 (m90) cc_final: 0.6398 (m90) REVERT: I 91 MET cc_start: 0.5021 (mmt) cc_final: 0.4820 (tpt) REVERT: K 97 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8401 (tm-30) REVERT: M 37 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8425 (ptp) REVERT: M 152 ARG cc_start: 0.6781 (mtt180) cc_final: 0.6498 (tpm170) REVERT: N 373 MET cc_start: 0.8275 (tpp) cc_final: 0.8016 (tpt) REVERT: O 139 MET cc_start: 0.4295 (tmm) cc_final: 0.3882 (tmm) REVERT: O 382 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8773 (p0) REVERT: P 203 MET cc_start: 0.7730 (mpp) cc_final: 0.7207 (mpp) REVERT: P 250 MET cc_start: 0.8606 (mpp) cc_final: 0.8262 (mpp) REVERT: Q 109 GLU cc_start: 0.2858 (tp30) cc_final: 0.2637 (tm-30) REVERT: Q 111 MET cc_start: 0.6244 (mmm) cc_final: 0.5993 (mmt) outliers start: 157 outliers final: 70 residues processed: 788 average time/residue: 0.2342 time to fit residues: 300.2731 Evaluate side-chains 577 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 492 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1131 LYS Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 127 TRP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 46 GLN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 193 TYR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain Q residue 80 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 405 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 383 optimal weight: 7.9990 chunk 40 optimal weight: 0.0170 chunk 61 optimal weight: 0.4980 chunk 304 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 738 GLN B 43 HIS ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN B1132 ASN D 7 ASN D 43 ASN D 112 GLN E 210 GLN H 46 GLN K 45 HIS O 146 ASN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN ** Q 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.091536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067999 restraints weight = 129967.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070516 restraints weight = 61140.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072176 restraints weight = 37950.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073224 restraints weight = 27992.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.073883 restraints weight = 23139.853| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 40373 Z= 0.212 Angle : 0.794 45.216 54682 Z= 0.390 Chirality : 0.047 0.251 6156 Planarity : 0.005 0.089 6895 Dihedral : 11.249 153.165 5779 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 4.03 % Allowed : 15.36 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 4805 helix: 0.04 (0.12), residues: 1735 sheet: 0.05 (0.20), residues: 650 loop : -1.00 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 214 TYR 0.028 0.002 TYR H 97 PHE 0.036 0.002 PHE D 69 TRP 0.030 0.002 TRP G 201 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (40351) covalent geometry : angle 0.73918 / 0.39 (54658) hydrogen bonds : bond 0.05169 / 3.43 ( 1559) hydrogen bonds : angle 5.35568 / 3.81 ( 4395) metal coordination : bond 0.00800 / 0.43 ( 22) metal coordination : angle 13.85644 / 6.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 521 time to evaluate : 1.337 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: symmetry clash REVERT: A 128 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: A 240 MET cc_start: 0.8262 (mtp) cc_final: 0.7866 (mtm) REVERT: A 312 PHE cc_start: 0.9521 (OUTLIER) cc_final: 0.9088 (t80) REVERT: A 970 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8302 (mtmm) REVERT: A 1228 GLU cc_start: 0.8062 (tt0) cc_final: 0.7862 (tt0) REVERT: A 1236 MET cc_start: 0.8541 (mtp) cc_final: 0.8259 (mtm) REVERT: A 1270 GLU cc_start: 0.7462 (tp30) cc_final: 0.7218 (tm-30) REVERT: B 459 PHE cc_start: 0.7616 (m-10) cc_final: 0.7376 (m-10) REVERT: B 506 MET cc_start: 0.7700 (mpp) cc_final: 0.7420 (mpp) REVERT: B 733 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9251 (pp) REVERT: C 91 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8147 (ttpp) REVERT: C 141 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7601 (ttm-80) REVERT: D 40 GLN cc_start: 0.8723 (tm130) cc_final: 0.8274 (pm20) REVERT: D 59 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6808 (mtm-85) REVERT: D 89 HIS cc_start: 0.7560 (t70) cc_final: 0.7318 (t-90) REVERT: D 99 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6072 (tt) REVERT: E 151 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7291 (ttm) REVERT: F 61 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8039 (mt-10) REVERT: F 100 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7857 (mmt90) REVERT: F 125 ILE cc_start: 0.8989 (pt) cc_final: 0.8702 (pt) REVERT: G 6 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: G 7 MET cc_start: 0.7989 (mtp) cc_final: 0.7542 (mtp) REVERT: G 184 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7348 (t80) REVERT: G 185 THR cc_start: 0.8931 (p) cc_final: 0.8716 (p) REVERT: H 37 MET cc_start: 0.7918 (mmm) cc_final: 0.7242 (mmp) REVERT: H 146 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8361 (ttpt) REVERT: I 74 HIS cc_start: 0.6594 (m90) cc_final: 0.6305 (m90) REVERT: L 51 ARG cc_start: 0.8438 (ttm110) cc_final: 0.8025 (ttp-110) REVERT: M 37 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8567 (ptp) REVERT: O 55 CYS cc_start: 0.9114 (m) cc_final: 0.8809 (m) REVERT: O 239 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8976 (mp) REVERT: O 270 MET cc_start: 0.8888 (ttp) cc_final: 0.8454 (ptp) REVERT: O 382 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.8783 (p0) REVERT: O 398 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8023 (mtp) REVERT: O 513 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: P 203 MET cc_start: 0.8131 (mpp) cc_final: 0.7302 (mpp) REVERT: P 217 TRP cc_start: 0.4209 (t-100) cc_final: 0.3614 (m100) REVERT: P 250 MET cc_start: 0.8617 (mpp) cc_final: 0.8316 (mpp) REVERT: P 273 VAL cc_start: -0.1325 (OUTLIER) cc_final: -0.1528 (t) outliers start: 173 outliers final: 101 residues processed: 642 average time/residue: 0.2289 time to fit residues: 243.3222 Evaluate side-chains 563 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 445 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1223 TYR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 127 TRP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 322 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 513 GLU Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 307 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 461 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 chunk 240 optimal weight: 0.5980 chunk 431 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 350 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 408 GLN ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN B1132 ASN C 305 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.091439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067813 restraints weight = 130253.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070374 restraints weight = 61545.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072032 restraints weight = 38176.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073084 restraints weight = 28146.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073748 restraints weight = 23251.652| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40373 Z= 0.155 Angle : 0.727 33.514 54682 Z= 0.355 Chirality : 0.045 0.246 6156 Planarity : 0.005 0.070 6895 Dihedral : 11.024 153.746 5767 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 3.78 % Allowed : 16.39 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 4805 helix: 0.28 (0.12), residues: 1743 sheet: 0.09 (0.20), residues: 658 loop : -0.90 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG Q 108 TYR 0.026 0.002 TYR D 52 PHE 0.025 0.001 PHE D 69 TRP 0.019 0.002 TRP G 201 HIS 0.007 0.001 HIS P 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (40351) covalent geometry : angle 0.68024 / 0.35 (54658) hydrogen bonds : bond 0.04505 / 2.97 ( 1559) hydrogen bonds : angle 5.10022 / 3.61 ( 4395) metal coordination : bond 0.00619 / 0.36 ( 22) metal coordination : angle 12.21528 / 6.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 498 time to evaluate : 1.366 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: A 312 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9041 (t80) REVERT: A 332 MET cc_start: 0.8516 (mmm) cc_final: 0.8249 (mmm) REVERT: A 953 MET cc_start: 0.8651 (mtp) cc_final: 0.8406 (mtp) REVERT: A 970 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8112 (mtmm) REVERT: A 1194 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7810 (mm-30) REVERT: A 1275 MET cc_start: 0.9044 (mmm) cc_final: 0.8736 (mmm) REVERT: B 733 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9282 (pp) REVERT: B 1015 MET cc_start: 0.8668 (mtm) cc_final: 0.8344 (mtm) REVERT: C 91 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8103 (ttpp) REVERT: C 141 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7795 (ttm-80) REVERT: C 212 MET cc_start: 0.8958 (mtm) cc_final: 0.8473 (mtm) REVERT: D 15 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: D 23 LEU cc_start: 0.8764 (tt) cc_final: 0.8374 (mm) REVERT: D 40 GLN cc_start: 0.8700 (tm130) cc_final: 0.8304 (pm20) REVERT: D 59 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6785 (mpp80) REVERT: D 89 HIS cc_start: 0.7569 (t70) cc_final: 0.7327 (t-90) REVERT: D 99 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6274 (tt) REVERT: E 72 MET cc_start: 0.8349 (ttp) cc_final: 0.8027 (ttm) REVERT: E 94 MET cc_start: 0.8355 (tmm) cc_final: 0.8053 (tmm) REVERT: E 151 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7276 (ttm) REVERT: F 57 MET cc_start: 0.8971 (tmm) cc_final: 0.8748 (tmm) REVERT: F 61 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8121 (mt-10) REVERT: F 100 ARG cc_start: 0.8235 (mmt90) cc_final: 0.8024 (mmt90) REVERT: F 125 ILE cc_start: 0.9032 (pt) cc_final: 0.8827 (pt) REVERT: G 6 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: G 7 MET cc_start: 0.8061 (mtp) cc_final: 0.7481 (mtt) REVERT: G 184 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7307 (t80) REVERT: H 5 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9039 (mm) REVERT: H 37 MET cc_start: 0.7833 (mmm) cc_final: 0.7290 (mmp) REVERT: H 146 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8370 (ttpt) REVERT: I 96 LYS cc_start: 0.7503 (tppt) cc_final: 0.7062 (tppt) REVERT: L 41 TYR cc_start: 0.8497 (t80) cc_final: 0.8031 (t80) REVERT: L 51 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8115 (ttp-110) REVERT: N 350 MET cc_start: 0.8601 (tpp) cc_final: 0.7659 (mpp) REVERT: O 98 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8662 (mp) REVERT: O 139 MET cc_start: 0.4199 (tmm) cc_final: 0.3898 (tmm) REVERT: O 239 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.9005 (mp) REVERT: O 270 MET cc_start: 0.8718 (ttp) cc_final: 0.8514 (ptp) REVERT: O 382 ASP cc_start: 0.9354 (OUTLIER) cc_final: 0.8863 (p0) REVERT: O 398 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7481 (mtp) REVERT: O 404 MET cc_start: 0.8431 (mmt) cc_final: 0.8051 (mmm) REVERT: O 513 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: P 203 MET cc_start: 0.8161 (mpp) cc_final: 0.7362 (mpp) REVERT: P 217 TRP cc_start: 0.4149 (t-100) cc_final: 0.3602 (m100) REVERT: P 237 THR cc_start: 0.3947 (t) cc_final: 0.3710 (m) REVERT: P 250 MET cc_start: 0.8736 (mpp) cc_final: 0.8502 (mpp) REVERT: P 256 LYS cc_start: 0.8007 (tttp) cc_final: 0.7618 (tptt) outliers start: 162 outliers final: 98 residues processed: 613 average time/residue: 0.2336 time to fit residues: 237.4740 Evaluate side-chains 561 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 445 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1223 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 127 TRP Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 329 LEU Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 513 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 472 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 286 optimal weight: 0.0770 chunk 348 optimal weight: 4.9990 chunk 329 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 251 optimal weight: 0.5980 chunk 323 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 HIS B1121 ASN B1132 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN K 45 HIS N 278 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.090220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066386 restraints weight = 130214.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068907 restraints weight = 61780.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070531 restraints weight = 38509.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071597 restraints weight = 28543.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072235 restraints weight = 23614.732| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40373 Z= 0.169 Angle : 0.707 35.893 54682 Z= 0.345 Chirality : 0.045 0.297 6156 Planarity : 0.005 0.066 6895 Dihedral : 10.820 153.939 5763 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 4.06 % Allowed : 16.78 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 4805 helix: 0.47 (0.12), residues: 1742 sheet: 0.11 (0.20), residues: 677 loop : -0.87 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 108 TYR 0.027 0.002 TYR H 97 PHE 0.039 0.002 PHE D 69 TRP 0.027 0.002 TRP G 201 HIS 0.030 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (40351) covalent geometry : angle 0.66160 / 0.34 (54658) hydrogen bonds : bond 0.04236 / 2.79 ( 1559) hydrogen bonds : angle 5.01362 / 3.55 ( 4395) metal coordination : bond 0.00668 / 0.40 ( 22) metal coordination : angle 11.88439 / 5.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 477 time to evaluate : 1.571 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.9483 (OUTLIER) cc_final: 0.9041 (t80) REVERT: A 332 MET cc_start: 0.8611 (mmm) cc_final: 0.8318 (mmm) REVERT: A 518 GLU cc_start: 0.8484 (tt0) cc_final: 0.8023 (tt0) REVERT: A 970 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8195 (mtmm) REVERT: A 1131 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8706 (ttmt) REVERT: A 1194 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7905 (mm-30) REVERT: A 1236 MET cc_start: 0.8665 (mtp) cc_final: 0.8348 (mtm) REVERT: A 1253 GLU cc_start: 0.8502 (tp30) cc_final: 0.8125 (tt0) REVERT: A 1275 MET cc_start: 0.8990 (mmm) cc_final: 0.8705 (mmm) REVERT: B 649 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.9011 (p) REVERT: B 696 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 733 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9297 (pp) REVERT: B 1015 MET cc_start: 0.8599 (mtm) cc_final: 0.8313 (mtm) REVERT: C 91 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8131 (ttpp) REVERT: C 141 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7854 (ttm-80) REVERT: D 15 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: D 40 GLN cc_start: 0.8734 (tm130) cc_final: 0.8383 (pm20) REVERT: D 59 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6743 (mpp80) REVERT: D 89 HIS cc_start: 0.7599 (t70) cc_final: 0.7343 (t-90) REVERT: D 99 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6304 (tt) REVERT: E 72 MET cc_start: 0.8303 (ttp) cc_final: 0.8018 (ttm) REVERT: E 94 MET cc_start: 0.8532 (tmm) cc_final: 0.8163 (tmm) REVERT: E 151 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7298 (ttm) REVERT: F 61 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8255 (mt-10) REVERT: F 100 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7825 (mmt90) REVERT: F 125 ILE cc_start: 0.9057 (pt) cc_final: 0.8770 (pt) REVERT: G 6 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: G 7 MET cc_start: 0.8041 (mtp) cc_final: 0.7378 (mtt) REVERT: G 73 ARG cc_start: 0.8641 (ptp-170) cc_final: 0.8188 (mtm110) REVERT: G 184 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7101 (t80) REVERT: H 5 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9052 (mm) REVERT: H 37 MET cc_start: 0.7727 (mmm) cc_final: 0.7118 (mmm) REVERT: H 146 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8434 (ttpt) REVERT: I 49 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8609 (p) REVERT: L 41 TYR cc_start: 0.8663 (t80) cc_final: 0.8253 (t80) REVERT: L 51 ARG cc_start: 0.8453 (ttm110) cc_final: 0.8126 (ttp-110) REVERT: M 53 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8816 (tm-30) REVERT: N 350 MET cc_start: 0.8590 (tpp) cc_final: 0.7675 (mpp) REVERT: O 98 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8817 (mt) REVERT: O 139 MET cc_start: 0.4074 (tmm) cc_final: 0.3874 (tmm) REVERT: O 404 MET cc_start: 0.8291 (mmt) cc_final: 0.8016 (mmm) REVERT: O 513 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: O 524 GLU cc_start: 0.8773 (tp30) cc_final: 0.8555 (tp30) REVERT: P 203 MET cc_start: 0.8181 (mpp) cc_final: 0.7474 (mpp) REVERT: P 217 TRP cc_start: 0.4396 (t-100) cc_final: 0.3633 (m100) REVERT: P 237 THR cc_start: 0.4144 (t) cc_final: 0.3894 (m) REVERT: Q 57 MET cc_start: 0.8618 (ptp) cc_final: 0.8357 (ptp) outliers start: 174 outliers final: 119 residues processed: 610 average time/residue: 0.2431 time to fit residues: 245.5950 Evaluate side-chains 567 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 429 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1131 LYS Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1223 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 322 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 513 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain Q residue 41 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 398 optimal weight: 10.0000 chunk 334 optimal weight: 0.9990 chunk 393 optimal weight: 8.9990 chunk 446 optimal weight: 6.9990 chunk 345 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 332 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 304 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN M 149 HIS N 270 GLN O 34 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.088671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.064758 restraints weight = 130334.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067234 restraints weight = 62657.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068857 restraints weight = 39372.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069873 restraints weight = 29275.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070521 restraints weight = 24330.579| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40373 Z= 0.198 Angle : 0.732 36.504 54682 Z= 0.352 Chirality : 0.045 0.300 6156 Planarity : 0.005 0.062 6895 Dihedral : 10.700 153.987 5762 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 4.22 % Allowed : 17.44 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 4805 helix: 0.59 (0.12), residues: 1753 sheet: 0.00 (0.19), residues: 688 loop : -0.85 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 214 TYR 0.024 0.002 TYR H 97 PHE 0.028 0.002 PHE I 94 TRP 0.023 0.002 TRP G 201 HIS 0.009 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (40351) covalent geometry : angle 0.68128 / 0.35 (54658) hydrogen bonds : bond 0.04188 / 2.75 ( 1559) hydrogen bonds : angle 4.98774 / 3.53 ( 4395) metal coordination : bond 0.00763 / 0.45 ( 22) metal coordination : angle 12.81041 / 6.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 461 time to evaluate : 1.641 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: A 116 MET cc_start: 0.8034 (mtm) cc_final: 0.7820 (mtm) REVERT: A 312 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.9002 (t80) REVERT: A 332 MET cc_start: 0.8688 (mmm) cc_final: 0.8333 (mmm) REVERT: A 518 GLU cc_start: 0.8532 (tt0) cc_final: 0.8240 (tt0) REVERT: A 1107 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8543 (ttmm) REVERT: A 1112 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 1236 MET cc_start: 0.8571 (mtp) cc_final: 0.8265 (mtm) REVERT: A 1349 MET cc_start: 0.9040 (mmm) cc_final: 0.8790 (mmm) REVERT: B 243 MET cc_start: 0.8365 (mmm) cc_final: 0.7749 (mmm) REVERT: B 451 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8469 (tpt) REVERT: B 649 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8993 (p) REVERT: B 1015 MET cc_start: 0.8652 (mtm) cc_final: 0.8329 (mtm) REVERT: B 1116 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: C 212 MET cc_start: 0.8883 (mtm) cc_final: 0.8329 (mtm) REVERT: D 15 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: D 40 GLN cc_start: 0.8686 (tm130) cc_final: 0.8423 (pm20) REVERT: D 47 TYR cc_start: 0.8083 (t80) cc_final: 0.7881 (t80) REVERT: D 59 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6625 (mpp80) REVERT: D 89 HIS cc_start: 0.7607 (t70) cc_final: 0.7339 (t-90) REVERT: D 99 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6395 (tt) REVERT: E 72 MET cc_start: 0.8273 (ttp) cc_final: 0.7988 (ttm) REVERT: E 94 MET cc_start: 0.8517 (tmm) cc_final: 0.8192 (tmm) REVERT: E 151 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7306 (ttm) REVERT: F 57 MET cc_start: 0.8868 (tmm) cc_final: 0.8554 (tmm) REVERT: G 6 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: G 7 MET cc_start: 0.8018 (mtp) cc_final: 0.7390 (mtt) REVERT: G 73 ARG cc_start: 0.8810 (ptp-170) cc_final: 0.8547 (mtm110) REVERT: G 184 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7127 (t80) REVERT: H 5 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9054 (mm) REVERT: H 37 MET cc_start: 0.7567 (mmm) cc_final: 0.7015 (mmm) REVERT: H 146 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8464 (ttpt) REVERT: I 49 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8550 (p) REVERT: K 53 ASN cc_start: 0.8994 (t0) cc_final: 0.8725 (t0) REVERT: L 15 MET cc_start: 0.6926 (tpp) cc_final: 0.6460 (tpp) REVERT: L 41 TYR cc_start: 0.8732 (t80) cc_final: 0.8210 (t80) REVERT: L 51 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8140 (ttp-110) REVERT: O 98 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8732 (mp) REVERT: O 404 MET cc_start: 0.8229 (mmt) cc_final: 0.7989 (mmm) REVERT: O 513 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: O 524 GLU cc_start: 0.8833 (tp30) cc_final: 0.8619 (tp30) REVERT: P 203 MET cc_start: 0.8216 (mpp) cc_final: 0.7541 (mpp) REVERT: P 217 TRP cc_start: 0.4131 (t-100) cc_final: 0.3758 (m100) REVERT: P 237 THR cc_start: 0.4517 (t) cc_final: 0.4283 (m) REVERT: P 250 MET cc_start: 0.8635 (mpp) cc_final: 0.8360 (mpp) outliers start: 181 outliers final: 129 residues processed: 595 average time/residue: 0.2373 time to fit residues: 232.9963 Evaluate side-chains 565 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 422 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1223 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 322 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 513 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 307 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 322 optimal weight: 9.9990 chunk 439 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 426 optimal weight: 1.9990 chunk 348 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.087678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063624 restraints weight = 130299.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066062 restraints weight = 63012.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067667 restraints weight = 39766.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068675 restraints weight = 29619.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069314 restraints weight = 24656.334| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40373 Z= 0.205 Angle : 0.742 38.905 54682 Z= 0.354 Chirality : 0.045 0.250 6156 Planarity : 0.005 0.060 6895 Dihedral : 10.625 154.106 5760 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 4.03 % Allowed : 18.02 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 4805 helix: 0.62 (0.12), residues: 1757 sheet: 0.02 (0.20), residues: 670 loop : -0.84 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 213 TYR 0.021 0.002 TYR H 97 PHE 0.025 0.002 PHE D 69 TRP 0.021 0.002 TRP G 201 HIS 0.011 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (40351) covalent geometry : angle 0.68428 / 0.35 (54658) hydrogen bonds : bond 0.04123 / 2.71 ( 1559) hydrogen bonds : angle 4.98358 / 3.54 ( 4395) metal coordination : bond 0.00793 / 0.44 ( 22) metal coordination : angle 13.75272 / 6.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 454 time to evaluate : 1.700 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 116 MET cc_start: 0.8008 (mtm) cc_final: 0.7775 (mtm) REVERT: A 312 PHE cc_start: 0.9474 (OUTLIER) cc_final: 0.9017 (t80) REVERT: A 332 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8334 (mmm) REVERT: A 1112 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 1158 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7842 (pp) REVERT: A 1236 MET cc_start: 0.8612 (mtp) cc_final: 0.8320 (mtm) REVERT: A 1275 MET cc_start: 0.8893 (mmm) cc_final: 0.8442 (mmp) REVERT: B 59 MET cc_start: 0.8712 (ppp) cc_final: 0.8418 (tmm) REVERT: B 243 MET cc_start: 0.8379 (mmm) cc_final: 0.7739 (mmm) REVERT: B 649 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9028 (p) REVERT: B 1015 MET cc_start: 0.8637 (mtm) cc_final: 0.8330 (mtm) REVERT: D 15 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: D 40 GLN cc_start: 0.8649 (tm130) cc_final: 0.8423 (pm20) REVERT: D 47 TYR cc_start: 0.8089 (t80) cc_final: 0.7868 (t80) REVERT: D 89 HIS cc_start: 0.7605 (t70) cc_final: 0.7290 (t-90) REVERT: E 72 MET cc_start: 0.8266 (ttp) cc_final: 0.7997 (ttm) REVERT: E 94 MET cc_start: 0.8476 (tmm) cc_final: 0.8188 (tmm) REVERT: E 151 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7364 (ttm) REVERT: F 61 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8158 (mt-10) REVERT: G 6 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: G 7 MET cc_start: 0.8198 (mtp) cc_final: 0.7724 (mtp) REVERT: G 9 ASP cc_start: 0.7632 (t0) cc_final: 0.7117 (m-30) REVERT: G 73 ARG cc_start: 0.8846 (ptp-170) cc_final: 0.8571 (mtm110) REVERT: G 184 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7089 (t80) REVERT: H 5 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9059 (mm) REVERT: H 37 MET cc_start: 0.7435 (mmm) cc_final: 0.7107 (mmm) REVERT: H 146 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8488 (ttpt) REVERT: I 49 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8532 (p) REVERT: K 53 ASN cc_start: 0.9085 (t0) cc_final: 0.8808 (t0) REVERT: L 41 TYR cc_start: 0.8706 (t80) cc_final: 0.8273 (t80) REVERT: L 51 ARG cc_start: 0.8477 (ttm110) cc_final: 0.8098 (ttp-110) REVERT: M 214 ARG cc_start: 0.8296 (mmp80) cc_final: 0.8085 (mmp80) REVERT: N 350 MET cc_start: 0.8638 (tpp) cc_final: 0.8364 (mmm) REVERT: O 55 CYS cc_start: 0.9166 (m) cc_final: 0.8757 (m) REVERT: O 79 CYS cc_start: 0.8559 (p) cc_final: 0.8008 (p) REVERT: O 98 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8762 (mp) REVERT: O 513 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: O 524 GLU cc_start: 0.8854 (tp30) cc_final: 0.8634 (tp30) REVERT: P 203 MET cc_start: 0.8133 (mpp) cc_final: 0.7598 (mpp) REVERT: P 217 TRP cc_start: 0.4014 (t-100) cc_final: 0.3645 (m100) REVERT: P 250 MET cc_start: 0.8820 (mpp) cc_final: 0.8494 (mpp) outliers start: 173 outliers final: 129 residues processed: 582 average time/residue: 0.2407 time to fit residues: 232.4168 Evaluate side-chains 557 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 416 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1223 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 322 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 513 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 307 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 1 optimal weight: 5.9990 chunk 449 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 470 optimal weight: 10.0000 chunk 409 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 397 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 967 GLN B 220 GLN B 408 GLN ** B 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN B1132 ASN C 268 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN O 27 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.088151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064234 restraints weight = 130042.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066712 restraints weight = 62440.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068335 restraints weight = 39251.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.069338 restraints weight = 29160.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069997 restraints weight = 24280.622| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 40373 Z= 0.144 Angle : 0.726 37.257 54682 Z= 0.345 Chirality : 0.044 0.225 6156 Planarity : 0.004 0.060 6895 Dihedral : 10.541 153.258 5760 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 3.50 % Allowed : 19.04 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 4805 helix: 0.70 (0.13), residues: 1760 sheet: -0.04 (0.19), residues: 685 loop : -0.77 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 284 TYR 0.022 0.001 TYR O 141 PHE 0.023 0.001 PHE G 104 TRP 0.017 0.001 TRP G 201 HIS 0.009 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (40351) covalent geometry : angle 0.67174 / 0.34 (54658) hydrogen bonds : bond 0.03874 / 2.54 ( 1559) hydrogen bonds : angle 4.85466 / 3.45 ( 4395) metal coordination : bond 0.00543 / 0.30 ( 22) metal coordination : angle 13.13344 / 6.58 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 471 time to evaluate : 1.590 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 312 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.8997 (t80) REVERT: A 332 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8350 (mmm) REVERT: A 912 MET cc_start: 0.8478 (mmm) cc_final: 0.7887 (tpt) REVERT: A 970 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8312 (mtmm) REVERT: A 1112 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8113 (tt0) REVERT: A 1236 MET cc_start: 0.8562 (mtp) cc_final: 0.8280 (mtm) REVERT: A 1275 MET cc_start: 0.8849 (mmm) cc_final: 0.8626 (mmm) REVERT: A 1349 MET cc_start: 0.8983 (mmm) cc_final: 0.8622 (mmm) REVERT: B 59 MET cc_start: 0.8629 (ppp) cc_final: 0.8375 (tmm) REVERT: B 334 TYR cc_start: 0.8818 (t80) cc_final: 0.8424 (t80) REVERT: B 649 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.9033 (p) REVERT: B 1015 MET cc_start: 0.8633 (mtm) cc_final: 0.8318 (mtm) REVERT: B 1036 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 1116 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: D 13 ASN cc_start: 0.7861 (m-40) cc_final: 0.7253 (m110) REVERT: D 15 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: D 47 TYR cc_start: 0.8126 (t80) cc_final: 0.7917 (t80) REVERT: D 52 TYR cc_start: 0.8390 (t80) cc_final: 0.7017 (t80) REVERT: D 59 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6911 (mpp80) REVERT: D 89 HIS cc_start: 0.7569 (t70) cc_final: 0.6971 (t-90) REVERT: E 72 MET cc_start: 0.8294 (ttp) cc_final: 0.7979 (ttm) REVERT: E 94 MET cc_start: 0.8439 (tmm) cc_final: 0.8137 (tmm) REVERT: E 151 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7326 (ttm) REVERT: F 57 MET cc_start: 0.8828 (tmm) cc_final: 0.8548 (tmm) REVERT: G 6 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: G 7 MET cc_start: 0.8205 (mtp) cc_final: 0.7634 (mtt) REVERT: G 9 ASP cc_start: 0.7682 (t0) cc_final: 0.7134 (m-30) REVERT: G 45 CYS cc_start: 0.8201 (m) cc_final: 0.7971 (t) REVERT: G 73 ARG cc_start: 0.8827 (ptp-170) cc_final: 0.8535 (mtm110) REVERT: G 116 GLN cc_start: 0.5180 (OUTLIER) cc_final: 0.4238 (pm20) REVERT: G 184 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7103 (t80) REVERT: H 5 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9065 (mm) REVERT: H 37 MET cc_start: 0.7337 (mmm) cc_final: 0.7077 (mmm) REVERT: H 146 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8516 (ttpt) REVERT: I 49 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8518 (p) REVERT: I 78 TYR cc_start: 0.3927 (t80) cc_final: 0.3158 (t80) REVERT: K 53 ASN cc_start: 0.9063 (t0) cc_final: 0.8789 (t0) REVERT: K 104 MET cc_start: 0.8665 (mmm) cc_final: 0.8185 (mmm) REVERT: L 41 TYR cc_start: 0.8701 (t80) cc_final: 0.8179 (t80) REVERT: L 51 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8114 (ttp-110) REVERT: O 55 CYS cc_start: 0.9174 (m) cc_final: 0.8768 (m) REVERT: O 79 CYS cc_start: 0.8603 (p) cc_final: 0.8012 (p) REVERT: O 98 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8741 (mp) REVERT: O 524 GLU cc_start: 0.8892 (tp30) cc_final: 0.8655 (tp30) REVERT: P 203 MET cc_start: 0.8052 (mpp) cc_final: 0.7568 (mpp) REVERT: P 250 MET cc_start: 0.8837 (mpp) cc_final: 0.8517 (mpp) outliers start: 150 outliers final: 112 residues processed: 579 average time/residue: 0.2425 time to fit residues: 233.7642 Evaluate side-chains 556 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 429 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 395 HIS Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 307 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 207 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 412 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 408 optimal weight: 20.0000 chunk 341 optimal weight: 3.9990 chunk 413 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 GLN A1278 HIS ** B 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN I 99 ASN ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 310 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 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 = 0.3723 r_free = 0.3723 target = 0.085950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062001 restraints weight = 131858.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064382 restraints weight = 63839.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065956 restraints weight = 40439.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066925 restraints weight = 30195.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067563 restraints weight = 25196.975| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 40373 Z= 0.251 Angle : 0.797 42.242 54682 Z= 0.379 Chirality : 0.046 0.266 6156 Planarity : 0.005 0.071 6895 Dihedral : 10.591 153.839 5759 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 3.45 % Allowed : 19.58 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.12), residues: 4805 helix: 0.64 (0.12), residues: 1760 sheet: -0.13 (0.20), residues: 680 loop : -0.81 (0.13), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 284 TYR 0.022 0.002 TYR O 141 PHE 0.036 0.002 PHE D 69 TRP 0.028 0.002 TRP I 59 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 (40351) covalent geometry : angle 0.73480 / 0.38 (54658) hydrogen bonds : bond 0.04263 / 2.80 ( 1559) hydrogen bonds : angle 5.04603 / 3.59 ( 4395) metal coordination : bond 0.00985 / 0.54 ( 22) metal coordination : angle 14.76566 / 7.37 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 423 time to evaluate : 1.708 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 312 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.8983 (t80) REVERT: A 332 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8327 (mmm) REVERT: A 1112 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8165 (mt-10) REVERT: A 1236 MET cc_start: 0.8647 (mtp) cc_final: 0.8350 (mtm) REVERT: A 1349 MET cc_start: 0.9084 (mmm) cc_final: 0.8796 (mmm) REVERT: B 59 MET cc_start: 0.8628 (ppp) cc_final: 0.8403 (tmm) REVERT: B 611 MET cc_start: 0.8786 (mmm) cc_final: 0.8478 (mmm) REVERT: B 832 MET cc_start: 0.8095 (mmm) cc_final: 0.7870 (mmm) REVERT: B 877 ASP cc_start: 0.7141 (m-30) cc_final: 0.6721 (t70) REVERT: B 1015 MET cc_start: 0.8623 (mtm) cc_final: 0.8292 (mtm) REVERT: B 1116 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: C 212 MET cc_start: 0.8953 (mtm) cc_final: 0.8456 (mtm) REVERT: D 15 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: D 47 TYR cc_start: 0.8111 (t80) cc_final: 0.7907 (t80) REVERT: D 52 TYR cc_start: 0.8447 (t80) cc_final: 0.7270 (t80) REVERT: D 59 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6766 (mpp80) REVERT: D 89 HIS cc_start: 0.7491 (t70) cc_final: 0.7257 (t-90) REVERT: E 72 MET cc_start: 0.8283 (ttp) cc_final: 0.8063 (ttm) REVERT: E 94 MET cc_start: 0.8420 (tmm) cc_final: 0.8180 (tmm) REVERT: E 151 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7458 (ttm) REVERT: F 61 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8490 (mt-10) REVERT: G 6 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: G 7 MET cc_start: 0.8264 (mtp) cc_final: 0.7665 (mtt) REVERT: G 9 ASP cc_start: 0.7567 (t0) cc_final: 0.6989 (m-30) REVERT: G 73 ARG cc_start: 0.8831 (ptp-170) cc_final: 0.8609 (mtm110) REVERT: G 184 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7260 (t80) REVERT: H 5 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9056 (mm) REVERT: H 37 MET cc_start: 0.7362 (mmm) cc_final: 0.7018 (mmm) REVERT: H 146 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8534 (ttpt) REVERT: L 41 TYR cc_start: 0.8740 (t80) cc_final: 0.8322 (t80) REVERT: L 51 ARG cc_start: 0.8494 (ttm110) cc_final: 0.8130 (ttp-110) REVERT: M 152 ARG cc_start: 0.6650 (mtt180) cc_final: 0.6442 (ptt-90) REVERT: O 55 CYS cc_start: 0.9098 (m) cc_final: 0.8670 (m) REVERT: O 79 CYS cc_start: 0.8640 (p) cc_final: 0.8089 (p) REVERT: O 98 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8728 (mp) REVERT: O 524 GLU cc_start: 0.8879 (tp30) cc_final: 0.8666 (tp30) REVERT: P 203 MET cc_start: 0.8111 (mpp) cc_final: 0.7571 (mpp) REVERT: P 250 MET cc_start: 0.8797 (mpp) cc_final: 0.8479 (mpp) outliers start: 148 outliers final: 120 residues processed: 537 average time/residue: 0.2486 time to fit residues: 221.4997 Evaluate side-chains 530 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 400 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1040 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 322 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 239 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 307 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 406 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 334 optimal weight: 0.8980 chunk 385 optimal weight: 7.9990 chunk 461 optimal weight: 0.0470 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 GLN B 408 GLN B 686 GLN ** B 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN I 99 ASN M 53 GLN M 200 HIS O 155 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.087748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063881 restraints weight = 129815.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066368 restraints weight = 61822.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067994 restraints weight = 38697.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069022 restraints weight = 28692.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069670 restraints weight = 23768.299| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40373 Z= 0.130 Angle : 0.744 40.790 54682 Z= 0.352 Chirality : 0.044 0.273 6156 Planarity : 0.005 0.073 6895 Dihedral : 10.512 153.464 5759 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 2.59 % Allowed : 20.54 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.21 (0.12), residues: 4805 helix: 0.72 (0.13), residues: 1780 sheet: -0.02 (0.20), residues: 670 loop : -0.79 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 419 TYR 0.030 0.001 TYR O 422 PHE 0.027 0.001 PHE D 69 TRP 0.025 0.001 TRP I 59 HIS 0.013 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (40351) covalent geometry : angle 0.68779 / 0.35 (54658) hydrogen bonds : bond 0.03803 / 2.49 ( 1559) hydrogen bonds : angle 4.84304 / 3.45 ( 4395) metal coordination : bond 0.00482 / 0.27 ( 22) metal coordination : angle 13.60992 / 6.86 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9610 Ramachandran restraints generated. 4805 Oldfield, 0 Emsley, 4805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 450 time to evaluate : 1.505 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: A 312 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.9012 (t80) REVERT: A 332 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8497 (mmm) REVERT: A 1112 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8190 (tt0) REVERT: A 1349 MET cc_start: 0.9005 (mmm) cc_final: 0.8755 (mmm) REVERT: B 59 MET cc_start: 0.8562 (ppp) cc_final: 0.8352 (tmm) REVERT: B 611 MET cc_start: 0.8672 (mmm) cc_final: 0.8470 (mmm) REVERT: B 832 MET cc_start: 0.8026 (mmm) cc_final: 0.7786 (mmm) REVERT: B 877 ASP cc_start: 0.7024 (m-30) cc_final: 0.6617 (t70) REVERT: B 1015 MET cc_start: 0.8611 (mtm) cc_final: 0.8269 (mtm) REVERT: B 1116 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: C 212 MET cc_start: 0.8802 (mtm) cc_final: 0.8341 (mtm) REVERT: D 15 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: D 47 TYR cc_start: 0.8101 (t80) cc_final: 0.7900 (t80) REVERT: D 52 TYR cc_start: 0.8367 (t80) cc_final: 0.7224 (t80) REVERT: D 89 HIS cc_start: 0.7485 (t70) cc_final: 0.7255 (t-90) REVERT: E 72 MET cc_start: 0.8237 (ttp) cc_final: 0.7974 (ttm) REVERT: E 94 MET cc_start: 0.8399 (tmm) cc_final: 0.8112 (tmm) REVERT: E 151 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7291 (ttm) REVERT: G 6 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: G 7 MET cc_start: 0.8327 (mtp) cc_final: 0.7670 (mtp) REVERT: G 9 ASP cc_start: 0.7766 (t0) cc_final: 0.7254 (m-30) REVERT: G 37 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7678 (mtmt) REVERT: G 73 ARG cc_start: 0.8763 (ptp-170) cc_final: 0.8465 (mtm110) REVERT: G 116 GLN cc_start: 0.5188 (OUTLIER) cc_final: 0.4116 (pm20) REVERT: G 184 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7117 (t80) REVERT: H 5 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9078 (mm) REVERT: H 37 MET cc_start: 0.7253 (mmm) cc_final: 0.7029 (mmm) REVERT: H 146 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8488 (ttpt) REVERT: K 53 ASN cc_start: 0.9052 (t0) cc_final: 0.8806 (t0) REVERT: L 41 TYR cc_start: 0.8590 (t80) cc_final: 0.8174 (t80) REVERT: L 51 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8113 (ttp-110) REVERT: O 55 CYS cc_start: 0.9071 (m) cc_final: 0.8635 (m) REVERT: O 79 CYS cc_start: 0.8618 (p) cc_final: 0.8025 (p) REVERT: O 98 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8720 (mp) REVERT: O 139 MET cc_start: 0.4448 (tmm) cc_final: 0.4215 (tmm) REVERT: O 524 GLU cc_start: 0.8895 (tp30) cc_final: 0.8659 (tp30) REVERT: P 203 MET cc_start: 0.7996 (mpp) cc_final: 0.7583 (mpp) REVERT: P 207 ASN cc_start: 0.8036 (p0) cc_final: 0.7762 (t0) REVERT: P 250 MET cc_start: 0.8828 (mpp) cc_final: 0.8519 (mpp) REVERT: P 293 PHE cc_start: 0.6848 (m-80) cc_final: 0.6510 (m-10) REVERT: Q 85 GLU cc_start: 0.3363 (OUTLIER) cc_final: 0.3146 (tp30) outliers start: 111 outliers final: 86 residues processed: 531 average time/residue: 0.2451 time to fit residues: 216.3729 Evaluate side-chains 514 residues out of total 4293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 417 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1168 HIS Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1131 TYR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 215 ASP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 380 VAL Chi-restraints excluded: chain O residue 382 ASP Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain Q residue 85 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 184 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 453 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 396 optimal weight: 0.4980 chunk 195 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 372 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 686 GLN B 903 GLN I 99 ASN O 155 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.085810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061890 restraints weight = 131879.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064296 restraints weight = 63402.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065882 restraints weight = 39928.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066882 restraints weight = 29750.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.067519 restraints weight = 24737.179| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 40373 Z= 0.227 Angle : 0.795 42.079 54682 Z= 0.375 Chirality : 0.046 0.277 6156 Planarity : 0.005 0.067 6895 Dihedral : 10.498 154.040 5755 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 2.75 % Allowed : 20.63 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 4805 helix: 0.69 (0.12), residues: 1772 sheet: -0.12 (0.20), residues: 677 loop : -0.78 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 407 TYR 0.030 0.002 TYR H 97 PHE 0.028 0.002 PHE D 69 TRP 0.026 0.002 TRP I 59 HIS 0.010 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (40351) covalent geometry : angle 0.73461 / 0.37 (54658) hydrogen bonds : bond 0.04050 / 2.65 ( 1559) hydrogen bonds : angle 4.96079 / 3.53 ( 4395) metal coordination : bond 0.00857 / 0.48 ( 22) metal coordination : angle 14.50664 / 7.28 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8504.51 seconds wall clock time: 147 minutes 43.30 seconds (8863.30 seconds total)