Starting phenix.real_space_refine on Fri Mar 6 20:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o4k_12721/03_2026/7o4k_12721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o4k_12721/03_2026/7o4k_12721.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/7o4k_12721/03_2026/7o4k_12721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o4k_12721/03_2026/7o4k_12721.map" model { file = "/net/cci-nas-00/data/ceres_data/7o4k_12721/03_2026/7o4k_12721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o4k_12721/03_2026/7o4k_12721.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= 0.027 sd= 0.977 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: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 10 6.06 5 P 22 5.49 5 Mg 1 5.21 5 S 202 5.16 5 Be 1 3.05 5 C 21697 2.51 5 N 5849 2.21 5 O 6475 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 158 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34264 Number of models: 1 Model: "" Number of chains: 25 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1081 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "4" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2267 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} Chain breaks: 2 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2786 Classifications: {'peptide': 355} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 333} Chain breaks: 1 Chain: "7" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4889 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 24, 'TRANS': 583} Chain breaks: 1 Chain: "A" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1298 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 10 Chain: "B" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 569 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Chain: "D" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1305 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 228 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 2 Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "N" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "W" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2532 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Chain: "X" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1094 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain breaks: 1 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" 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: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 52.255 89.308 110.935 1.00 61.92 S ATOM 1265 SG CYS 0 156 46.922 88.513 114.660 1.00 71.41 S ATOM 1080 SG CYS 0 133 48.713 94.417 112.999 1.00 66.77 S ATOM 1566 SG CYS 0 191 51.804 91.445 117.238 1.00 62.83 S ATOM 13933 SG CYS 3 13 37.561 119.989 65.296 1.00106.17 S ATOM 13954 SG CYS 3 16 38.737 119.365 61.697 1.00104.70 S ATOM 14149 SG CYS 3 39 40.214 122.232 63.705 1.00104.87 S ATOM 14170 SG CYS 3 42 36.665 122.440 62.505 1.00105.96 S ATOM 14102 SG CYS 3 34 30.897 125.475 74.362 1.00104.99 S ATOM 14260 SG CYS 3 54 30.224 124.304 70.752 1.00107.16 S ATOM 14298 SG CYS 3 59 27.402 124.114 73.377 1.00117.67 S ATOM 16955 SG CYS 4 289 101.195 49.137 131.691 1.00 82.91 S ATOM 16974 SG CYS 4 292 104.736 49.595 133.037 1.00 81.75 S ATOM 17066 SG CYS 4 305 102.205 47.646 135.039 1.00101.46 S ATOM 17084 SG CYS 4 308 101.815 51.406 134.692 1.00100.16 S ATOM 19751 SG CYS 6 349 105.282 32.142 117.946 1.00 87.94 S ATOM 19772 SG CYS 6 352 103.282 29.826 115.662 1.00101.87 S ATOM 19851 SG CYS 6 363 104.164 33.311 114.520 1.00 85.86 S ATOM 19870 SG CYS 6 366 101.610 32.826 117.324 1.00 94.45 S ATOM 20172 SG CYS 6 403 132.009 67.799 129.976 1.00 95.69 S ATOM 20195 SG CYS 6 406 133.976 66.777 126.889 1.00 83.95 S ATOM 20381 SG CYS 6 437 131.232 69.390 126.603 1.00 94.08 S ATOM 20402 SG CYS 6 440 130.338 65.759 127.215 1.00 85.29 S ATOM 20314 SG CYS 6 429 121.660 65.384 136.585 1.00100.90 S ATOM 20337 SG CYS 6 432 124.991 64.128 137.960 1.00 98.91 S ATOM 20495 SG CYS 6 451 123.986 63.219 134.454 1.00 80.80 S ATOM 20512 SG CYS 6 454 122.074 61.726 137.419 1.00 86.05 S ATOM 19650 SG CYS 6 336 109.055 33.158 104.173 1.00107.56 S ATOM 19662 SG CYS 6 338 107.878 36.008 106.476 1.00100.79 S ATOM 19810 SG CYS 6 357 111.611 35.360 105.974 1.00 87.54 S ATOM 25753 SG CYS A 107 76.965 112.371 38.449 1.00 81.89 S ATOM 25777 SG CYS A 110 75.910 114.160 41.628 1.00 78.01 S ATOM 25866 SG CYS A 148 79.490 112.825 41.236 1.00 93.14 S ATOM 26004 SG CYS A 167 76.470 110.452 41.663 1.00 92.18 S ATOM 26843 SG CYS B1163 52.410 143.197 35.667 1.00 52.45 S ATOM 26861 SG CYS B1166 54.003 140.347 33.461 1.00 51.55 S ATOM 26986 SG CYS B1182 50.255 140.533 34.173 1.00 45.94 S ATOM 27005 SG CYS B1185 52.756 139.651 36.915 1.00 55.21 S ATOM 31598 SG CYS W 124 25.685 136.816 32.775 1.00 99.73 S ATOM 31619 SG CYS W 127 28.867 135.876 31.091 1.00100.42 S ATOM 31804 SG CYS W 149 28.166 139.570 32.102 1.00 90.79 S ATOM 31824 SG CYS W 152 26.368 137.920 29.154 1.00 96.55 S Time building chain proxies: 7.32, per 1000 atoms: 0.21 Number of scatterers: 34264 At special positions: 0 Unit cell: (190.05, 197.4, 165.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 10 29.99 Fe 4 26.01 S 202 16.00 P 22 15.00 Mg 1 11.99 F 3 9.00 O 6475 8.00 N 5849 7.00 C 21697 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " Number of angles added : 54 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8070 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 37 sheets defined 50.8% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain '0' and resid 18 through 35 removed outlier: 3.521A pdb=" N TYR 0 22 " --> pdb=" O TYR 0 18 " (cutoff:3.500A) Processing helix chain '0' and resid 48 through 63 Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 110 through 114 Processing helix chain '0' and resid 125 through 138 Processing helix chain '0' and resid 139 through 148 Processing helix chain '0' and resid 156 through 163 removed outlier: 3.765A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) Processing helix chain '0' and resid 164 through 165 No H-bonds generated for 'chain '0' and resid 164 through 165' Processing helix chain '0' and resid 166 through 170 Processing helix chain '0' and resid 177 through 189 Processing helix chain '0' and resid 191 through 198 Processing helix chain '0' and resid 210 through 215 Processing helix chain '0' and resid 215 through 224 removed outlier: 3.699A pdb=" N GLU 0 220 " --> pdb=" O PRO 0 216 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG 0 221 " --> pdb=" O LYS 0 217 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) Processing helix chain '0' and resid 239 through 247 removed outlier: 3.957A pdb=" N VAL 0 243 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 278 Processing helix chain '0' and resid 279 through 292 removed outlier: 3.652A pdb=" N GLY 0 292 " --> pdb=" O LYS 0 288 " (cutoff:3.500A) Processing helix chain '0' and resid 294 through 299 Processing helix chain '0' and resid 322 through 326 Processing helix chain '0' and resid 327 through 345 Processing helix chain '0' and resid 346 through 348 No H-bonds generated for 'chain '0' and resid 346 through 348' Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 376 removed outlier: 3.515A pdb=" N LEU 0 374 " --> pdb=" O GLU 0 370 " (cutoff:3.500A) Processing helix chain '0' and resid 376 through 388 Processing helix chain '0' and resid 396 through 410 removed outlier: 3.954A pdb=" N LYS 0 400 " --> pdb=" O PHE 0 396 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP 0 401 " --> pdb=" O THR 0 397 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE 0 402 " --> pdb=" O ALA 0 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER 0 410 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) Processing helix chain '0' and resid 446 through 453 Processing helix chain '0' and resid 467 through 473 removed outlier: 3.558A pdb=" N ARG 0 471 " --> pdb=" O ASP 0 467 " (cutoff:3.500A) Processing helix chain '0' and resid 509 through 513 removed outlier: 3.656A pdb=" N ARG 0 513 " --> pdb=" O PHE 0 510 " (cutoff:3.500A) Processing helix chain '0' and resid 515 through 533 removed outlier: 3.767A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 543 through 558 Processing helix chain '0' and resid 558 through 565 removed outlier: 3.875A pdb=" N GLU 0 562 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 Processing helix chain '0' and resid 613 through 617 Processing helix chain '0' and resid 632 through 647 Processing helix chain '0' and resid 649 through 667 removed outlier: 3.519A pdb=" N HIS 0 661 " --> pdb=" O ASP 0 657 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 693 removed outlier: 3.984A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 694 through 699 Processing helix chain '0' and resid 702 through 706 removed outlier: 3.701A pdb=" N LEU 0 706 " --> pdb=" O ASP 0 703 " (cutoff:3.500A) Processing helix chain '0' and resid 709 through 725 Processing helix chain '0' and resid 729 through 734 removed outlier: 3.555A pdb=" N GLU 0 734 " --> pdb=" O LYS 0 731 " (cutoff:3.500A) Processing helix chain '0' and resid 740 through 752 Processing helix chain '1' and resid 93 through 121 removed outlier: 4.046A pdb=" N ARG 1 121 " --> pdb=" O TYR 1 117 " (cutoff:3.500A) Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 177 through 188 removed outlier: 3.536A pdb=" N LEU 1 185 " --> pdb=" O GLN 1 181 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY 1 187 " --> pdb=" O SER 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 200 Processing helix chain '1' and resid 205 through 210 Processing helix chain '1' and resid 213 through 225 removed outlier: 4.031A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 232 through 237 removed outlier: 4.101A pdb=" N THR 1 236 " --> pdb=" O ASN 1 232 " (cutoff:3.500A) Processing helix chain '1' and resid 253 through 263 Processing helix chain '1' and resid 263 through 272 removed outlier: 3.523A pdb=" N LYS 1 267 " --> pdb=" O TYR 1 263 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 290 Processing helix chain '1' and resid 291 through 297 Processing helix chain '1' and resid 308 through 313 removed outlier: 3.775A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) Processing helix chain '1' and resid 313 through 330 removed outlier: 4.505A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 334 through 337 Processing helix chain '1' and resid 338 through 344 removed outlier: 4.000A pdb=" N ASN 1 342 " --> pdb=" O ASP 1 338 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE 1 343 " --> pdb=" O LEU 1 339 " (cutoff:3.500A) Processing helix chain '1' and resid 355 through 359 Processing helix chain '1' and resid 370 through 390 removed outlier: 3.842A pdb=" N ILE 1 374 " --> pdb=" O GLY 1 370 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 419 removed outlier: 3.704A pdb=" N GLU 1 418 " --> pdb=" O ASP 1 414 " (cutoff:3.500A) Processing helix chain '1' and resid 465 through 483 Processing helix chain '1' and resid 486 through 490 Processing helix chain '1' and resid 495 through 515 removed outlier: 3.511A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 569 Processing helix chain '1' and resid 572 through 574 No H-bonds generated for 'chain '1' and resid 572 through 574' Processing helix chain '1' and resid 575 through 605 Processing helix chain '1' and resid 608 through 616 Processing helix chain '1' and resid 616 through 638 Processing helix chain '2' and resid 6 through 17 Processing helix chain '2' and resid 18 through 26 removed outlier: 3.765A pdb=" N ARG 2 24 " --> pdb=" O GLN 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 39 removed outlier: 3.603A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU 2 39 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 52 removed outlier: 4.314A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 66 removed outlier: 3.738A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 84 removed outlier: 3.567A pdb=" N GLN 2 75 " --> pdb=" O LYS 2 71 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN 2 76 " --> pdb=" O LEU 2 72 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 114 Processing helix chain '2' and resid 134 through 152 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 194 removed outlier: 3.746A pdb=" N GLN 2 190 " --> pdb=" O ASN 2 186 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 211 removed outlier: 4.108A pdb=" N LEU 2 203 " --> pdb=" O GLN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 231 removed outlier: 3.520A pdb=" N MET 2 227 " --> pdb=" O HIS 2 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY 2 229 " --> pdb=" O ILE 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 255 removed outlier: 3.924A pdb=" N ILE 2 248 " --> pdb=" O GLU 2 244 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP 2 255 " --> pdb=" O GLN 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 280 removed outlier: 3.506A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER 2 280 " --> pdb=" O LEU 2 276 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 361 Processing helix chain '2' and resid 379 through 389 removed outlier: 3.700A pdb=" N ASN 2 389 " --> pdb=" O ARG 2 385 " (cutoff:3.500A) Processing helix chain '2' and resid 392 through 403 Processing helix chain '2' and resid 405 through 421 removed outlier: 3.821A pdb=" N GLU 2 421 " --> pdb=" O GLU 2 417 " (cutoff:3.500A) Processing helix chain '2' and resid 434 through 449 removed outlier: 3.917A pdb=" N VAL 2 438 " --> pdb=" O PRO 2 434 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 478 Processing helix chain '2' and resid 497 through 507 Processing helix chain '3' and resid 40 through 48 Processing helix chain '3' and resid 64 through 68 Processing helix chain '3' and resid 75 through 90 Processing helix chain '3' and resid 95 through 100 Processing helix chain '3' and resid 102 through 123 Processing helix chain '3' and resid 125 through 139 removed outlier: 3.557A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU 3 139 " --> pdb=" O THR 3 135 " (cutoff:3.500A) Processing helix chain '4' and resid 33 through 44 removed outlier: 3.787A pdb=" N THR 4 39 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 68 removed outlier: 3.792A pdb=" N LYS 4 52 " --> pdb=" O GLY 4 48 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 115 through 139 removed outlier: 4.138A pdb=" N THR 4 124 " --> pdb=" O ASN 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 166 Processing helix chain '4' and resid 189 through 191 No H-bonds generated for 'chain '4' and resid 189 through 191' Processing helix chain '4' and resid 192 through 206 removed outlier: 3.881A pdb=" N PHE 4 201 " --> pdb=" O MET 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 221 through 230 removed outlier: 3.649A pdb=" N GLN 4 226 " --> pdb=" O THR 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 243 through 251 removed outlier: 3.888A pdb=" N TYR 4 247 " --> pdb=" O GLY 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 262 removed outlier: 3.714A pdb=" N ARG 4 259 " --> pdb=" O PRO 4 256 " (cutoff:3.500A) Proline residue: 4 260 - end of helix Processing helix chain '4' and resid 300 through 304 removed outlier: 3.903A pdb=" N LYS 4 304 " --> pdb=" O PRO 4 301 " (cutoff:3.500A) Processing helix chain '4' and resid 313 through 322 removed outlier: 3.576A pdb=" N LEU 4 320 " --> pdb=" O VAL 4 316 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 27 Processing helix chain '5' and resid 45 through 58 removed outlier: 4.276A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 5 56 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 61 No H-bonds generated for 'chain '5' and resid 59 through 61' Processing helix chain '6' and resid 97 through 114 removed outlier: 3.676A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN 6 114 " --> pdb=" O THR 6 110 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 3.935A pdb=" N GLU 6 138 " --> pdb=" O ALA 6 135 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 164 Processing helix chain '6' and resid 188 through 200 removed outlier: 3.849A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 221 Processing helix chain '6' and resid 246 through 257 removed outlier: 3.659A pdb=" N THR 6 250 " --> pdb=" O ASP 6 246 " (cutoff:3.500A) Processing helix chain '6' and resid 270 through 281 Processing helix chain '6' and resid 293 through 306 removed outlier: 4.258A pdb=" N THR 6 306 " --> pdb=" O ASN 6 302 " (cutoff:3.500A) Processing helix chain '6' and resid 372 through 378 removed outlier: 3.594A pdb=" N LEU 6 376 " --> pdb=" O LEU 6 372 " (cutoff:3.500A) Processing helix chain '6' and resid 379 through 383 Processing helix chain '6' and resid 437 through 447 removed outlier: 3.602A pdb=" N VAL 6 442 " --> pdb=" O VAL 6 438 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 457 Processing helix chain '7' and resid 109 through 113 Processing helix chain '7' and resid 149 through 161 removed outlier: 3.838A pdb=" N ASP 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL 7 158 " --> pdb=" O GLN 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 176 through 188 removed outlier: 3.732A pdb=" N LEU 7 188 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) Processing helix chain '7' and resid 189 through 201 Processing helix chain '7' and resid 206 through 216 Processing helix chain '7' and resid 238 through 240 No H-bonds generated for 'chain '7' and resid 238 through 240' Processing helix chain '7' and resid 241 through 246 Processing helix chain '7' and resid 322 through 333 removed outlier: 3.636A pdb=" N LYS 7 328 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 7 332 " --> pdb=" O LYS 7 328 " (cutoff:3.500A) Processing helix chain '7' and resid 363 through 372 Processing helix chain '7' and resid 391 through 404 Processing helix chain '7' and resid 414 through 428 removed outlier: 3.505A pdb=" N CYS 7 428 " --> pdb=" O PHE 7 424 " (cutoff:3.500A) Processing helix chain '7' and resid 431 through 433 No H-bonds generated for 'chain '7' and resid 431 through 433' Processing helix chain '7' and resid 457 through 460 Processing helix chain '7' and resid 467 through 480 removed outlier: 3.893A pdb=" N LYS 7 472 " --> pdb=" O HIS 7 468 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL 7 473 " --> pdb=" O ASP 7 469 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG 7 480 " --> pdb=" O PHE 7 476 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 493 removed outlier: 3.505A pdb=" N VAL 7 493 " --> pdb=" O VAL 7 490 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 490 through 493' Processing helix chain '7' and resid 497 through 499 No H-bonds generated for 'chain '7' and resid 497 through 499' Processing helix chain '7' and resid 500 through 505 removed outlier: 3.726A pdb=" N ILE 7 505 " --> pdb=" O VAL 7 501 " (cutoff:3.500A) Processing helix chain '7' and resid 521 through 529 removed outlier: 4.314A pdb=" N ILE 7 524 " --> pdb=" O ASP 7 521 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY 7 525 " --> pdb=" O ASP 7 522 " (cutoff:3.500A) Processing helix chain '7' and resid 539 through 546 removed outlier: 3.506A pdb=" N LEU 7 543 " --> pdb=" O ASN 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 562 through 572 removed outlier: 4.199A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU 7 570 " --> pdb=" O TYR 7 566 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 573 through 583 removed outlier: 3.736A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET 7 583 " --> pdb=" O LEU 7 579 " (cutoff:3.500A) Processing helix chain '7' and resid 584 through 601 removed outlier: 3.605A pdb=" N PHE 7 588 " --> pdb=" O ASN 7 584 " (cutoff:3.500A) Processing helix chain '7' and resid 611 through 623 Processing helix chain '7' and resid 632 through 646 Processing helix chain '7' and resid 655 through 660 removed outlier: 4.501A pdb=" N THR 7 660 " --> pdb=" O VAL 7 657 " (cutoff:3.500A) Processing helix chain '7' and resid 679 through 688 removed outlier: 4.005A pdb=" N GLU 7 683 " --> pdb=" O SER 7 679 " (cutoff:3.500A) Processing helix chain '7' and resid 689 through 691 No H-bonds generated for 'chain '7' and resid 689 through 691' Processing helix chain '7' and resid 713 through 723 removed outlier: 4.023A pdb=" N TYR 7 717 " --> pdb=" O THR 7 713 " (cutoff:3.500A) Processing helix chain '7' and resid 725 through 730 Processing helix chain '7' and resid 752 through 767 removed outlier: 3.901A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.976A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1149 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'D' and resid 51 through 73 removed outlier: 3.507A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 removed outlier: 3.512A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'F' and resid 93 through 103 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'W' and resid 3 through 21 removed outlier: 3.576A pdb=" N ASP W 7 " --> pdb=" O ARG W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 35 Processing helix chain 'W' and resid 40 through 48 Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 90 through 118 Processing helix chain 'W' and resid 132 through 138 removed outlier: 4.049A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 179 Processing helix chain 'W' and resid 179 through 192 removed outlier: 3.502A pdb=" N LYS W 188 " --> pdb=" O ASP W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 203 Processing helix chain 'W' and resid 204 through 206 No H-bonds generated for 'chain 'W' and resid 204 through 206' Processing helix chain 'W' and resid 266 through 288 Processing helix chain 'W' and resid 291 through 296 removed outlier: 3.554A pdb=" N GLN W 296 " --> pdb=" O GLU W 292 " (cutoff:3.500A) Processing helix chain 'W' and resid 350 through 369 Processing helix chain 'X' and resid 188 through 198 Processing helix chain 'X' and resid 206 through 211 Processing helix chain 'X' and resid 217 through 227 Processing helix chain 'X' and resid 256 through 266 removed outlier: 3.998A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 281 Processing helix chain 'X' and resid 289 through 293 Processing sheet with id=AA1, first strand: chain '0' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain '0' and resid 174 through 176 removed outlier: 6.715A pdb=" N GLY 0 105 " --> pdb=" O PHE 0 176 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG 0 104 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE 0 207 " --> pdb=" O ARG 0 104 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 207 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N SER 0 209 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER 0 38 " --> pdb=" O ILE 0 458 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN 0 37 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN 0 480 " --> pdb=" O ASN 0 37 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE 0 39 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER 0 482 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU 0 41 " --> pdb=" O SER 0 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 250 through 253 Processing sheet with id=AA4, first strand: chain '0' and resid 492 through 497 removed outlier: 6.008A pdb=" N LEU 0 493 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU 0 681 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET 0 495 " --> pdb=" O LEU 0 681 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY 0 536 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU 0 621 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL 0 538 " --> pdb=" O LEU 0 621 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE 0 623 " --> pdb=" O VAL 0 538 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE 0 540 " --> pdb=" O ILE 0 623 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 4 through 9 Processing sheet with id=AA6, first strand: chain '1' and resid 86 through 90 removed outlier: 7.692A pdb=" N MET 1 59 " --> pdb=" O ALA 1 50 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ALA 1 50 " --> pdb=" O MET 1 59 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG 1 61 " --> pdb=" O LEU 1 48 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU 1 48 " --> pdb=" O ARG 1 61 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE 1 63 " --> pdb=" O ASP 1 46 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU 1 48 " --> pdb=" O VAL W 416 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 246 through 252 removed outlier: 5.909A pdb=" N VAL 1 247 " --> pdb=" O HIS W 261 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN W 263 " --> pdb=" O VAL 1 247 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL 1 249 " --> pdb=" O ASN W 263 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR W 265 " --> pdb=" O VAL 1 249 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU 1 251 " --> pdb=" O THR W 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '2' and resid 57 through 58 Processing sheet with id=AA9, first strand: chain '2' and resid 174 through 176 Processing sheet with id=AB1, first strand: chain '2' and resid 237 through 238 removed outlier: 3.654A pdb=" N TYR 2 237 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE 2 269 " --> pdb=" O TYR 2 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '2' and resid 339 through 341 removed outlier: 7.464A pdb=" N LEU 2 375 " --> pdb=" O LYS 2 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 481 through 485 removed outlier: 7.057A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS 5 39 " --> pdb=" O LEU 5 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 28 through 29 Processing sheet with id=AB5, first strand: chain '3' and resid 52 through 53 removed outlier: 3.553A pdb=" N ALA 3 52 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '4' and resid 82 through 87 removed outlier: 6.446A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ASP 4 211 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU 4 176 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL 4 178 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE 4 215 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR 4 180 " --> pdb=" O ILE 4 215 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU 4 236 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL 4 212 " --> pdb=" O LEU 4 236 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL 4 238 " --> pdb=" O VAL 4 212 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS 4 214 " --> pdb=" O VAL 4 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 295 through 296 removed outlier: 4.220A pdb=" N MET 6 369 " --> pdb=" O LYS 6 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '6' and resid 178 through 186 removed outlier: 6.341A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLN 6 184 " --> pdb=" O MET 6 169 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET 6 169 " --> pdb=" O GLN 6 184 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER 6 125 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU 6 233 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE 6 127 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL 6 235 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR 6 129 " --> pdb=" O VAL 6 235 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG 6 230 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS 6 262 " --> pdb=" O ARG 6 230 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL 6 232 " --> pdb=" O LYS 6 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU 6 264 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE 6 234 " --> pdb=" O LEU 6 264 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LYS 6 289 " --> pdb=" O VAL 6 261 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL 6 263 " --> pdb=" O LYS 6 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '6' and resid 326 through 335 removed outlier: 10.271A pdb=" N GLU 6 330 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) removed outlier: 11.158A pdb=" N TYR 6 347 " --> pdb=" O GLU 6 330 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N THR 6 332 " --> pdb=" O GLY 6 345 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY 6 345 " --> pdb=" O THR 6 332 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '6' and resid 390 through 391 removed outlier: 3.545A pdb=" N ALA 6 390 " --> pdb=" O ARG 6 428 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG 6 428 " --> pdb=" O ALA 6 390 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 132 through 134 removed outlier: 7.140A pdb=" N GLU 7 172 " --> pdb=" O ILE 7 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 223 through 228 removed outlier: 4.490A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 340 through 341 Processing sheet with id=AC5, first strand: chain '7' and resid 435 through 438 removed outlier: 6.725A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE 7 408 " --> pdb=" O ILE 7 486 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASP 7 488 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU 7 410 " --> pdb=" O ASP 7 488 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY 7 483 " --> pdb=" O ALA 7 507 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA 7 509 " --> pdb=" O GLY 7 483 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR 7 514 " --> pdb=" O ILE 7 384 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE 7 383 " --> pdb=" O LEU 7 535 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU 7 537 " --> pdb=" O ILE 7 383 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL 7 385 " --> pdb=" O GLU 7 537 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 651 through 653 removed outlier: 6.373A pdb=" N ILE 7 606 " --> pdb=" O ILE 7 671 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU 7 670 " --> pdb=" O TYR 7 706 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU 7 708 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN 7 672 " --> pdb=" O LEU 7 708 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N SER 7 710 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE 7 705 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS 7 734 " --> pdb=" O CYS 7 554 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AC8, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AC9, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.563A pdb=" N SER A 184 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1442 through 1445 Processing sheet with id=AD2, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD3, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AD5, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.953A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP G 55 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.518A pdb=" N THR G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 86 through 93 removed outlier: 3.525A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AD9, first strand: chain 'W' and resid 38 through 39 Processing sheet with id=AE1, first strand: chain 'X' and resid 230 through 234 removed outlier: 4.372A pdb=" N TYR X 243 " --> pdb=" O LEU X 233 " (cutoff:3.500A) 1587 hydrogen bonds defined for protein. 4491 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: 7.91 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 14189 1.43 - 1.64: 20396 1.64 - 1.85: 305 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 34902 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" F2 BEF 7 901 " pdb="BE BEF 7 901 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" F3 BEF 7 901 " pdb="BE BEF 7 901 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" F1 BEF 7 901 " pdb="BE BEF 7 901 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.65e+00 ... (remaining 34897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 46940 2.48 - 4.95: 225 4.95 - 7.43: 6 7.43 - 9.90: 6 9.90 - 12.38: 2 Bond angle restraints: 47179 Sorted by residual: angle pdb=" N VAL 1 495 " pdb=" CA VAL 1 495 " pdb=" C VAL 1 495 " ideal model delta sigma weight residual 112.96 108.60 4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" C1' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C3' ADP 7 903 " ideal model delta sigma weight residual 111.00 98.62 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N VAL 0 736 " pdb=" CA VAL 0 736 " pdb=" C VAL 0 736 " ideal model delta sigma weight residual 112.96 109.52 3.44 1.00e+00 1.00e+00 1.18e+01 angle pdb=" PA ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sigma weight residual 120.50 130.78 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N VAL 7 460 " pdb=" CA VAL 7 460 " pdb=" C VAL 7 460 " ideal model delta sigma weight residual 113.53 110.21 3.32 9.80e-01 1.04e+00 1.15e+01 ... (remaining 47174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 21005 35.57 - 71.15: 368 71.15 - 106.72: 41 106.72 - 142.29: 2 142.29 - 177.86: 1 Dihedral angle restraints: 21417 sinusoidal: 9037 harmonic: 12380 Sorted by residual: dihedral pdb=" O1B ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " pdb=" PA ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 117.86 -177.86 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 63.94 -123.94 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -169.82 109.82 1 2.00e+01 2.50e-03 3.21e+01 ... (remaining 21414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4418 0.042 - 0.084: 613 0.084 - 0.127: 337 0.127 - 0.169: 9 0.169 - 0.211: 1 Chirality restraints: 5378 Sorted by residual: chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE 7 745 " pdb=" N ILE 7 745 " pdb=" C ILE 7 745 " pdb=" CB ILE 7 745 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE 0 5 " pdb=" N ILE 0 5 " pdb=" C ILE 0 5 " pdb=" CB ILE 0 5 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 5375 not shown) Planarity restraints: 5947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS 0 614 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C HIS 0 614 " 0.048 2.00e-02 2.50e+03 pdb=" O HIS 0 614 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN 0 615 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 5 13 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO 5 14 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO 5 14 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 5 14 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN 3 31 " 0.024 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO 3 32 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO 3 32 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 3 32 " 0.021 5.00e-02 4.00e+02 ... (remaining 5944 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 221 2.58 - 3.16: 28701 3.16 - 3.74: 50662 3.74 - 4.32: 71727 4.32 - 4.90: 119600 Nonbonded interactions: 270911 Sorted by model distance: nonbonded pdb="MG MG 7 902 " pdb=" O3B ADP 7 903 " model vdw 2.001 2.170 nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.001 2.120 nonbonded pdb=" O ARG 7 130 " pdb=" NZ LYS 7 202 " model vdw 2.162 3.120 nonbonded pdb=" OH TYR W 21 " pdb=" OD2 ASP W 64 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR X 235 " pdb=" O ASP X 238 " model vdw 2.166 3.040 ... (remaining 270906 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.040 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.489 34947 Z= 0.288 Angle : 0.468 12.379 47245 Z= 0.264 Chirality : 0.038 0.211 5378 Planarity : 0.002 0.050 5947 Dihedral : 14.038 177.863 13347 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.05 (0.14), residues: 4122 helix: 1.91 (0.13), residues: 1879 sheet: -0.38 (0.23), residues: 550 loop : -0.24 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 144 TYR 0.009 0.001 TYR 7 581 PHE 0.009 0.001 PHE A 22 TRP 0.006 0.001 TRP 7 420 HIS 0.003 0.000 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00224 (34902) covalent geometry : angle 0.45764 (47179) hydrogen bonds : bond 0.21906 ( 1587) hydrogen bonds : angle 6.82087 ( 4491) metal coordination : bond 0.00228 ( 44) metal coordination : angle 2.62174 ( 66) Misc. bond : bond 0.48911 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 929 time to evaluate : 1.222 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: 0 34 VAL cc_start: 0.8645 (p) cc_final: 0.8219 (m) REVERT: 0 71 TYR cc_start: 0.8110 (t80) cc_final: 0.7769 (t80) REVERT: 0 90 MET cc_start: 0.7859 (mmm) cc_final: 0.7471 (mmp) REVERT: 0 91 ASP cc_start: 0.6794 (m-30) cc_final: 0.6577 (m-30) REVERT: 0 131 GLU cc_start: 0.5088 (tp30) cc_final: 0.4831 (pt0) REVERT: 0 135 ARG cc_start: 0.7237 (mtp85) cc_final: 0.6966 (mmm-85) REVERT: 0 136 MET cc_start: 0.8157 (mtm) cc_final: 0.7528 (mtt) REVERT: 0 142 LYS cc_start: 0.7870 (tttt) cc_final: 0.7431 (tttp) REVERT: 0 183 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7497 (mtpp) REVERT: 0 218 ILE cc_start: 0.8495 (pt) cc_final: 0.8222 (pt) REVERT: 0 236 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6553 (mt-10) REVERT: 0 259 ARG cc_start: 0.7406 (mtp85) cc_final: 0.7022 (mtm-85) REVERT: 0 365 GLN cc_start: 0.6526 (tt0) cc_final: 0.6214 (mt0) REVERT: 0 547 MET cc_start: 0.8309 (ttp) cc_final: 0.8080 (ttm) REVERT: 0 553 MET cc_start: 0.6281 (mmm) cc_final: 0.5776 (mtp) REVERT: 0 622 MET cc_start: 0.8460 (tpt) cc_final: 0.8186 (mmm) REVERT: 0 640 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7056 (mm-30) REVERT: 0 643 ARG cc_start: 0.7324 (ttp80) cc_final: 0.6964 (ttp80) REVERT: 0 675 ASP cc_start: 0.8219 (t0) cc_final: 0.7964 (t0) REVERT: 0 718 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7501 (mtpp) REVERT: 1 19 ASN cc_start: 0.7647 (t0) cc_final: 0.7399 (t0) REVERT: 1 29 TRP cc_start: 0.8617 (t60) cc_final: 0.8151 (t60) REVERT: 1 58 MET cc_start: 0.7121 (mtt) cc_final: 0.6839 (mtm) REVERT: 1 61 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6526 (ptm160) REVERT: 1 88 MET cc_start: 0.5175 (ttp) cc_final: 0.4669 (mtt) REVERT: 1 178 LEU cc_start: 0.8198 (mt) cc_final: 0.7926 (tp) REVERT: 1 238 LYS cc_start: 0.7537 (mttt) cc_final: 0.7284 (mmtm) REVERT: 1 299 GLU cc_start: 0.7467 (tt0) cc_final: 0.6609 (tt0) REVERT: 1 313 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6898 (mtm-85) REVERT: 1 318 ASP cc_start: 0.7018 (t0) cc_final: 0.6741 (t0) REVERT: 1 321 PHE cc_start: 0.7836 (m-10) cc_final: 0.7528 (m-80) REVERT: 1 364 ILE cc_start: 0.8062 (mm) cc_final: 0.7559 (mm) REVERT: 1 373 ASP cc_start: 0.6891 (t0) cc_final: 0.6508 (m-30) REVERT: 1 552 MET cc_start: 0.8482 (ttt) cc_final: 0.7811 (tpp) REVERT: 1 563 HIS cc_start: 0.8191 (m-70) cc_final: 0.7879 (m-70) REVERT: 1 581 LYS cc_start: 0.8574 (mttt) cc_final: 0.7733 (mptt) REVERT: 1 585 HIS cc_start: 0.8160 (m170) cc_final: 0.7895 (m90) REVERT: 1 597 PHE cc_start: 0.7638 (m-10) cc_final: 0.7166 (m-80) REVERT: 1 628 HIS cc_start: 0.8533 (t-90) cc_final: 0.8231 (t-90) REVERT: 2 13 TYR cc_start: 0.8324 (t80) cc_final: 0.8071 (t80) REVERT: 2 66 VAL cc_start: 0.9107 (t) cc_final: 0.8879 (p) REVERT: 2 81 MET cc_start: 0.7784 (mtp) cc_final: 0.7425 (mtm) REVERT: 2 97 MET cc_start: 0.6451 (mmm) cc_final: 0.6160 (tpp) REVERT: 2 138 TYR cc_start: 0.8030 (t80) cc_final: 0.7787 (t80) REVERT: 2 200 LEU cc_start: 0.7849 (mt) cc_final: 0.7604 (mt) REVERT: 2 277 MET cc_start: 0.7396 (tpp) cc_final: 0.6518 (tmm) REVERT: 2 344 ASN cc_start: 0.6915 (t0) cc_final: 0.6691 (t0) REVERT: 3 11 ASP cc_start: 0.8122 (t0) cc_final: 0.6803 (t0) REVERT: 3 20 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8066 (ttp80) REVERT: 3 33 GLU cc_start: 0.7135 (tp30) cc_final: 0.6619 (tm-30) REVERT: 3 35 TYR cc_start: 0.7514 (m-80) cc_final: 0.6947 (m-10) REVERT: 3 129 THR cc_start: 0.8474 (m) cc_final: 0.7998 (t) REVERT: 3 130 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6581 (mt-10) REVERT: 4 39 THR cc_start: 0.8671 (m) cc_final: 0.8386 (p) REVERT: 4 232 ASN cc_start: 0.8334 (t0) cc_final: 0.8082 (t0) REVERT: 4 323 LYS cc_start: 0.8792 (ptmt) cc_final: 0.8445 (ptmt) REVERT: 6 139 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8021 (mmmm) REVERT: 6 294 GLU cc_start: 0.7208 (tt0) cc_final: 0.6841 (tt0) REVERT: 6 450 ASN cc_start: 0.8666 (p0) cc_final: 0.8354 (p0) REVERT: 7 138 ASP cc_start: 0.6850 (m-30) cc_final: 0.6418 (p0) REVERT: 7 568 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6866 (tp30) REVERT: 7 663 ASP cc_start: 0.7070 (t0) cc_final: 0.6816 (t0) REVERT: 7 694 LYS cc_start: 0.7986 (tmtt) cc_final: 0.7678 (tppt) REVERT: 7 748 LEU cc_start: 0.8743 (mt) cc_final: 0.8538 (mt) REVERT: 7 762 GLU cc_start: 0.7571 (tp30) cc_final: 0.7245 (tp30) REVERT: A 112 LYS cc_start: 0.7607 (tttm) cc_final: 0.6941 (mtpp) REVERT: A 169 ASN cc_start: 0.8550 (m-40) cc_final: 0.7898 (m110) REVERT: A 175 ARG cc_start: 0.6853 (ptt90) cc_final: 0.6561 (ttp-110) REVERT: A 1444 MET cc_start: 0.7528 (mmm) cc_final: 0.7314 (mmm) REVERT: A 1454 MET cc_start: 0.5660 (tpp) cc_final: 0.5312 (mmm) REVERT: D 34 GLN cc_start: 0.7283 (mt0) cc_final: 0.6921 (pt0) REVERT: F 101 ILE cc_start: 0.7115 (mt) cc_final: 0.6740 (mm) REVERT: G 53 ASN cc_start: 0.7434 (m110) cc_final: 0.7156 (t0) REVERT: G 140 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7381 (ttmm) REVERT: W 81 SER cc_start: 0.6931 (p) cc_final: 0.6248 (m) REVERT: W 106 VAL cc_start: 0.7766 (t) cc_final: 0.7529 (m) REVERT: W 114 ASP cc_start: 0.7905 (m-30) cc_final: 0.7693 (t0) REVERT: W 135 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7098 (mm-30) REVERT: W 145 THR cc_start: 0.6913 (p) cc_final: 0.5777 (t) REVERT: W 156 LEU cc_start: 0.8513 (mm) cc_final: 0.8276 (mt) REVERT: W 180 GLN cc_start: 0.7384 (tp40) cc_final: 0.6880 (tp40) REVERT: W 181 PRO cc_start: 0.8689 (Cg_exo) cc_final: 0.8402 (Cg_endo) REVERT: W 193 ARG cc_start: 0.6612 (tpp80) cc_final: 0.6392 (tpp-160) REVERT: W 211 ASN cc_start: 0.6470 (m110) cc_final: 0.6046 (m110) REVERT: W 263 ASN cc_start: 0.7424 (t0) cc_final: 0.7123 (m110) REVERT: X 194 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7681 (ptmm) REVERT: X 203 LYS cc_start: 0.7731 (tptm) cc_final: 0.7385 (tptt) REVERT: X 239 LYS cc_start: 0.8553 (mmtp) cc_final: 0.8180 (mmmt) REVERT: X 284 LYS cc_start: 0.8324 (tttt) cc_final: 0.8071 (tmtt) outliers start: 0 outliers final: 0 residues processed: 929 average time/residue: 0.2221 time to fit residues: 329.1001 Evaluate side-chains 687 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.0170 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 ASN 1 105 GLN 1 262 ASN 1 352 ASN 1 488 GLN 1 510 ASN 1 563 HIS 2 19 GLN 2 85 HIS 2 206 GLN 2 500 GLN ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 225 GLN 5 55 ASN 6 164 ASN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 345 ASN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 548 HIS ** 7 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 672 GLN 7 685 GLN 7 738 HIS A 109 HIS A 282 ASN D 37 GLN D 157 GLN D 199 ASN F 100 GLN G 97 HIS G 113 HIS W 133 GLN W 169 GLN X 267 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.184047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.120724 restraints weight = 40295.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.119722 restraints weight = 27842.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.120945 restraints weight = 24901.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.121833 restraints weight = 21443.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.121810 restraints weight = 19540.718| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 34947 Z= 0.354 Angle : 0.753 20.198 47245 Z= 0.376 Chirality : 0.049 0.213 5378 Planarity : 0.005 0.069 5947 Dihedral : 8.661 141.979 4758 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.91 % Allowed : 9.56 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.22 (0.13), residues: 4122 helix: 0.98 (0.12), residues: 1933 sheet: -0.63 (0.22), residues: 536 loop : -0.47 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 75 TYR 0.041 0.002 TYR 0 208 PHE 0.034 0.002 PHE A 22 TRP 0.021 0.002 TRP X 214 HIS 0.014 0.002 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00853 (34902) covalent geometry : angle 0.73184 (47179) hydrogen bonds : bond 0.05498 ( 1587) hydrogen bonds : angle 5.13206 ( 4491) metal coordination : bond 0.01262 ( 44) metal coordination : angle 4.81654 ( 66) Misc. bond : bond 0.00526 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 748 time to evaluate : 1.450 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: 0 34 VAL cc_start: 0.8696 (p) cc_final: 0.8331 (m) REVERT: 0 79 ILE cc_start: 0.8386 (mt) cc_final: 0.8164 (mp) REVERT: 0 90 MET cc_start: 0.8276 (mmm) cc_final: 0.7898 (mmp) REVERT: 0 183 LYS cc_start: 0.7625 (ttmt) cc_final: 0.7352 (mtpp) REVERT: 0 218 ILE cc_start: 0.8771 (pt) cc_final: 0.8514 (pt) REVERT: 0 236 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6819 (mt-10) REVERT: 0 259 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7414 (mtm110) REVERT: 0 357 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7596 (ttpp) REVERT: 0 365 GLN cc_start: 0.6724 (tt0) cc_final: 0.6381 (mt0) REVERT: 0 531 LYS cc_start: 0.8273 (mttt) cc_final: 0.7993 (mttt) REVERT: 0 622 MET cc_start: 0.8916 (tpt) cc_final: 0.8443 (mmm) REVERT: 0 640 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7112 (mm-30) REVERT: 0 643 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6943 (ttp80) REVERT: 0 650 GLU cc_start: 0.7627 (mp0) cc_final: 0.7414 (mt-10) REVERT: 0 659 MET cc_start: 0.8527 (mmm) cc_final: 0.8217 (mmt) REVERT: 0 718 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7933 (mtpp) REVERT: 1 9 PHE cc_start: 0.7026 (t80) cc_final: 0.6739 (t80) REVERT: 1 19 ASN cc_start: 0.7648 (t0) cc_final: 0.7403 (t0) REVERT: 1 61 ARG cc_start: 0.7018 (ttp-110) cc_final: 0.6202 (mtp180) REVERT: 1 97 MET cc_start: 0.7356 (ttp) cc_final: 0.7119 (ttp) REVERT: 1 173 LYS cc_start: 0.6975 (mmtp) cc_final: 0.6410 (mtpt) REVERT: 1 178 LEU cc_start: 0.8368 (mt) cc_final: 0.8027 (tp) REVERT: 1 192 MET cc_start: 0.7877 (tpt) cc_final: 0.7554 (tpt) REVERT: 1 299 GLU cc_start: 0.7562 (tt0) cc_final: 0.7331 (tt0) REVERT: 1 318 ASP cc_start: 0.7075 (t0) cc_final: 0.6820 (t0) REVERT: 1 321 PHE cc_start: 0.7902 (m-10) cc_final: 0.7676 (m-80) REVERT: 1 343 ILE cc_start: 0.8096 (pt) cc_final: 0.7892 (pt) REVERT: 1 346 ASP cc_start: 0.7998 (t0) cc_final: 0.7581 (t70) REVERT: 1 373 ASP cc_start: 0.7190 (t0) cc_final: 0.6814 (m-30) REVERT: 1 580 LYS cc_start: 0.8187 (tttm) cc_final: 0.7817 (tttm) REVERT: 1 628 HIS cc_start: 0.8490 (t-90) cc_final: 0.8181 (t-90) REVERT: 2 87 LEU cc_start: 0.8262 (mp) cc_final: 0.7996 (mt) REVERT: 2 97 MET cc_start: 0.7038 (mmm) cc_final: 0.6565 (tpp) REVERT: 2 199 GLN cc_start: 0.8171 (tt0) cc_final: 0.7889 (tp-100) REVERT: 2 200 LEU cc_start: 0.8191 (mt) cc_final: 0.7977 (mt) REVERT: 2 227 MET cc_start: 0.7718 (ttp) cc_final: 0.6922 (ptt) REVERT: 2 247 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8315 (mtt-85) REVERT: 2 277 MET cc_start: 0.7754 (tpp) cc_final: 0.7225 (tpt) REVERT: 3 19 ASP cc_start: 0.7571 (t0) cc_final: 0.7226 (t0) REVERT: 3 37 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7318 (ttp80) REVERT: 3 69 LYS cc_start: 0.8240 (tppt) cc_final: 0.7978 (tppt) REVERT: 3 115 ASP cc_start: 0.6455 (t0) cc_final: 0.6208 (t0) REVERT: 3 130 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6522 (mt-10) REVERT: 4 51 ILE cc_start: 0.8773 (mm) cc_final: 0.8472 (mm) REVERT: 4 199 CYS cc_start: 0.8694 (m) cc_final: 0.8378 (m) REVERT: 4 229 ASP cc_start: 0.7982 (t0) cc_final: 0.7777 (t70) REVERT: 4 235 TYR cc_start: 0.9010 (t80) cc_final: 0.8721 (t80) REVERT: 4 237 HIS cc_start: 0.8252 (t-170) cc_final: 0.7972 (t-90) REVERT: 4 281 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7743 (mtm-85) REVERT: 4 323 LYS cc_start: 0.8675 (ptmt) cc_final: 0.8436 (tttp) REVERT: 6 134 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6944 (mm-30) REVERT: 6 252 ASP cc_start: 0.6889 (t0) cc_final: 0.6570 (t0) REVERT: 6 302 ASN cc_start: 0.7389 (t0) cc_final: 0.7059 (t0) REVERT: 6 303 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7671 (tm-30) REVERT: 6 341 LYS cc_start: 0.7872 (pttp) cc_final: 0.7670 (pttp) REVERT: 6 450 ASN cc_start: 0.8855 (p0) cc_final: 0.8548 (p0) REVERT: 7 124 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.6845 (ttm-80) REVERT: 7 138 ASP cc_start: 0.7009 (m-30) cc_final: 0.6593 (p0) REVERT: 7 190 THR cc_start: 0.7459 (m) cc_final: 0.7256 (m) REVERT: 7 235 GLU cc_start: 0.6425 (tt0) cc_final: 0.6152 (tm-30) REVERT: 7 381 SER cc_start: 0.8792 (m) cc_final: 0.8513 (p) REVERT: 7 520 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7265 (mp0) REVERT: 7 571 ARG cc_start: 0.7522 (ptp-170) cc_final: 0.7317 (ptp90) REVERT: 7 576 LYS cc_start: 0.8141 (mttt) cc_final: 0.7871 (mtmm) REVERT: 7 694 LYS cc_start: 0.8124 (tmtt) cc_final: 0.7798 (tppt) REVERT: A 112 LYS cc_start: 0.7981 (tttm) cc_final: 0.7410 (mtpp) REVERT: A 143 LYS cc_start: 0.7983 (tttt) cc_final: 0.7113 (mptt) REVERT: A 149 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6812 (tm-30) REVERT: A 169 ASN cc_start: 0.8737 (m-40) cc_final: 0.8271 (m110) REVERT: A 187 LYS cc_start: 0.7747 (pttt) cc_final: 0.7439 (pttm) REVERT: A 199 LEU cc_start: 0.8206 (tt) cc_final: 0.7887 (pp) REVERT: D 155 ARG cc_start: 0.7064 (mmm-85) cc_final: 0.6833 (mmm-85) REVERT: F 101 ILE cc_start: 0.7376 (mt) cc_final: 0.7062 (mm) REVERT: F 103 MET cc_start: 0.7183 (mtp) cc_final: 0.6349 (mtt) REVERT: G 140 LYS cc_start: 0.7839 (ttpp) cc_final: 0.7469 (ttmm) REVERT: W 24 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.6961 (p) REVERT: W 45 GLN cc_start: 0.8037 (tt0) cc_final: 0.7807 (tt0) REVERT: W 81 SER cc_start: 0.6676 (p) cc_final: 0.6030 (m) REVERT: W 106 VAL cc_start: 0.8068 (t) cc_final: 0.7820 (m) REVERT: W 114 ASP cc_start: 0.8092 (m-30) cc_final: 0.7631 (t0) REVERT: W 135 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7375 (mm-30) REVERT: W 145 THR cc_start: 0.7062 (p) cc_final: 0.6703 (t) REVERT: W 148 LEU cc_start: 0.6846 (mm) cc_final: 0.6140 (pp) REVERT: W 169 GLN cc_start: 0.8189 (mt0) cc_final: 0.7982 (mt0) REVERT: W 180 GLN cc_start: 0.7605 (tp40) cc_final: 0.7079 (tp40) REVERT: W 223 LYS cc_start: 0.8610 (tppt) cc_final: 0.8057 (tptp) REVERT: W 229 ARG cc_start: 0.6866 (mtt90) cc_final: 0.6556 (mtt90) REVERT: W 263 ASN cc_start: 0.7441 (t0) cc_final: 0.7078 (m110) REVERT: X 196 LEU cc_start: 0.8614 (mt) cc_final: 0.8215 (mt) REVERT: X 203 LYS cc_start: 0.7824 (tptm) cc_final: 0.7147 (ttpp) outliers start: 73 outliers final: 49 residues processed: 778 average time/residue: 0.2260 time to fit residues: 281.3103 Evaluate side-chains 745 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 695 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 325 ILE Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 436 HIS Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 218 LEU Chi-restraints excluded: chain 2 residue 432 VAL Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 226 VAL Chi-restraints excluded: chain 7 residue 330 CYS Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 371 SER Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 739 LEU Chi-restraints excluded: chain 7 residue 755 GLU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 250 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 168 optimal weight: 40.0000 chunk 391 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 363 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 180 optimal weight: 0.2980 chunk 253 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 0 113 ASN 0 265 ASN 0 692 GLN 1 105 GLN 1 468 GLN 2 85 HIS ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 227 HIS ** 6 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 376 ASN 7 491 HIS ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 592 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.186593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3283 r_free = 0.3283 target = 0.126264 restraints weight = 40166.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.125711 restraints weight = 38586.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.128466 restraints weight = 30932.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127042 restraints weight = 26847.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.127797 restraints weight = 23938.584| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34947 Z= 0.180 Angle : 0.587 17.527 47245 Z= 0.292 Chirality : 0.042 0.176 5378 Planarity : 0.004 0.051 5947 Dihedral : 8.438 123.406 4758 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.17 % Allowed : 12.41 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.34 (0.13), residues: 4122 helix: 1.15 (0.12), residues: 1929 sheet: -0.61 (0.23), residues: 531 loop : -0.47 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 756 TYR 0.021 0.002 TYR 0 208 PHE 0.021 0.002 PHE 7 316 TRP 0.011 0.001 TRP 1 284 HIS 0.008 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00428 (34902) covalent geometry : angle 0.56588 (47179) hydrogen bonds : bond 0.04549 ( 1587) hydrogen bonds : angle 4.70859 ( 4491) metal coordination : bond 0.00710 ( 44) metal coordination : angle 4.25717 ( 66) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 723 time to evaluate : 1.573 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: 0 34 VAL cc_start: 0.8694 (p) cc_final: 0.8249 (m) REVERT: 0 79 ILE cc_start: 0.8342 (mt) cc_final: 0.8113 (mp) REVERT: 0 142 LYS cc_start: 0.8059 (tttt) cc_final: 0.7554 (tttp) REVERT: 0 183 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7237 (mtpp) REVERT: 0 218 ILE cc_start: 0.8684 (pt) cc_final: 0.8423 (pt) REVERT: 0 236 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6706 (mt-10) REVERT: 0 254 THR cc_start: 0.8934 (m) cc_final: 0.8708 (p) REVERT: 0 262 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7021 (ttm-80) REVERT: 0 270 ARG cc_start: 0.7486 (tpt-90) cc_final: 0.7097 (mmm160) REVERT: 0 346 MET cc_start: 0.8699 (mmt) cc_final: 0.8433 (tpp) REVERT: 0 357 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7580 (ttpp) REVERT: 0 365 GLN cc_start: 0.6639 (tt0) cc_final: 0.6295 (mt0) REVERT: 0 622 MET cc_start: 0.8891 (tpt) cc_final: 0.8416 (mmm) REVERT: 0 640 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7029 (mm-30) REVERT: 0 643 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6877 (ttp80) REVERT: 0 645 ASN cc_start: 0.8158 (m-40) cc_final: 0.7946 (m110) REVERT: 0 650 GLU cc_start: 0.7557 (mp0) cc_final: 0.7283 (mt-10) REVERT: 1 97 MET cc_start: 0.7236 (ttp) cc_final: 0.6783 (ttp) REVERT: 1 173 LYS cc_start: 0.6945 (mmtp) cc_final: 0.6563 (mmtt) REVERT: 1 178 LEU cc_start: 0.8213 (mt) cc_final: 0.7945 (tp) REVERT: 1 238 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7513 (tppt) REVERT: 1 318 ASP cc_start: 0.7011 (t0) cc_final: 0.6699 (t0) REVERT: 1 321 PHE cc_start: 0.7875 (m-10) cc_final: 0.7663 (m-80) REVERT: 1 346 ASP cc_start: 0.7912 (t0) cc_final: 0.7494 (t70) REVERT: 1 373 ASP cc_start: 0.7092 (t0) cc_final: 0.6784 (m-30) REVERT: 1 560 PHE cc_start: 0.8594 (m-80) cc_final: 0.8339 (m-80) REVERT: 1 628 HIS cc_start: 0.8265 (t-90) cc_final: 0.7980 (t-90) REVERT: 2 48 MET cc_start: 0.8854 (tpp) cc_final: 0.8595 (tpp) REVERT: 2 222 LEU cc_start: 0.8855 (mt) cc_final: 0.8643 (mp) REVERT: 2 224 PHE cc_start: 0.7162 (t80) cc_final: 0.6870 (t80) REVERT: 2 254 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7790 (mtt180) REVERT: 2 277 MET cc_start: 0.7460 (tpp) cc_final: 0.6924 (tpt) REVERT: 2 433 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7984 (pp) REVERT: 3 11 ASP cc_start: 0.7795 (t0) cc_final: 0.7095 (t0) REVERT: 3 12 MET cc_start: 0.7251 (mtt) cc_final: 0.6707 (mtt) REVERT: 3 20 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7617 (ttp80) REVERT: 3 37 ARG cc_start: 0.7635 (mtp-110) cc_final: 0.7229 (ttp80) REVERT: 3 115 ASP cc_start: 0.6507 (t0) cc_final: 0.6166 (t0) REVERT: 3 128 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7116 (mttt) REVERT: 4 51 ILE cc_start: 0.8848 (mm) cc_final: 0.8591 (mm) REVERT: 4 229 ASP cc_start: 0.7866 (t0) cc_final: 0.7605 (t70) REVERT: 4 235 TYR cc_start: 0.8918 (t80) cc_final: 0.8668 (t80) REVERT: 4 237 HIS cc_start: 0.8243 (t-170) cc_final: 0.7989 (t-90) REVERT: 5 59 SER cc_start: 0.8077 (m) cc_final: 0.7704 (p) REVERT: 5 63 TYR cc_start: 0.8497 (t80) cc_final: 0.8279 (t80) REVERT: 6 134 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6838 (mm-30) REVERT: 6 139 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8136 (mmmm) REVERT: 6 215 GLU cc_start: 0.7766 (mm-30) cc_final: 0.6832 (mt-10) REVERT: 6 252 ASP cc_start: 0.6938 (t0) cc_final: 0.6656 (t0) REVERT: 6 302 ASN cc_start: 0.7225 (t0) cc_final: 0.6977 (m-40) REVERT: 6 303 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7588 (tm-30) REVERT: 6 450 ASN cc_start: 0.8711 (p0) cc_final: 0.8397 (p0) REVERT: 7 236 THR cc_start: 0.8203 (p) cc_final: 0.7786 (t) REVERT: 7 313 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6738 (p) REVERT: 7 381 SER cc_start: 0.8698 (m) cc_final: 0.8387 (p) REVERT: 7 454 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8470 (m) REVERT: 7 571 ARG cc_start: 0.7460 (ptp-170) cc_final: 0.7203 (ptp90) REVERT: 7 576 LYS cc_start: 0.8013 (mttt) cc_final: 0.7672 (mtmm) REVERT: 7 694 LYS cc_start: 0.7976 (tmtt) cc_final: 0.7705 (tppt) REVERT: A 15 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7443 (mttt) REVERT: A 112 LYS cc_start: 0.8071 (tttm) cc_final: 0.7442 (mtpp) REVERT: A 143 LYS cc_start: 0.7944 (tttt) cc_final: 0.7225 (mptt) REVERT: A 169 ASN cc_start: 0.8715 (m-40) cc_final: 0.8297 (m110) REVERT: A 199 LEU cc_start: 0.8120 (tt) cc_final: 0.7830 (pp) REVERT: D 180 LEU cc_start: 0.8168 (mt) cc_final: 0.7916 (mt) REVERT: F 101 ILE cc_start: 0.7377 (mt) cc_final: 0.7092 (mm) REVERT: F 103 MET cc_start: 0.7202 (mtp) cc_final: 0.6360 (mtt) REVERT: G 31 LEU cc_start: 0.8553 (mt) cc_final: 0.8340 (mp) REVERT: G 140 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7513 (ttmm) REVERT: W 53 GLU cc_start: 0.6856 (tt0) cc_final: 0.6632 (mt-10) REVERT: W 106 VAL cc_start: 0.8064 (t) cc_final: 0.7802 (m) REVERT: W 114 ASP cc_start: 0.7962 (m-30) cc_final: 0.7566 (t0) REVERT: W 130 LYS cc_start: 0.6635 (mttp) cc_final: 0.6353 (mttm) REVERT: W 135 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7344 (mm-30) REVERT: W 141 ASN cc_start: 0.5877 (p0) cc_final: 0.5605 (m-40) REVERT: W 145 THR cc_start: 0.6933 (p) cc_final: 0.6556 (p) REVERT: W 180 GLN cc_start: 0.7776 (tp40) cc_final: 0.7019 (tp40) REVERT: W 223 LYS cc_start: 0.8555 (tppt) cc_final: 0.8104 (tptp) REVERT: W 285 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.7001 (mmm160) REVERT: X 203 LYS cc_start: 0.7892 (tptm) cc_final: 0.7671 (tptm) REVERT: X 322 LYS cc_start: 0.8166 (tttp) cc_final: 0.7949 (tttt) outliers start: 83 outliers final: 53 residues processed: 759 average time/residue: 0.2328 time to fit residues: 281.0126 Evaluate side-chains 730 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 672 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 105 GLN Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 238 LYS Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 432 VAL Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 74 ASP Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 330 CYS Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 371 SER Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 755 GLU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 285 ARG Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 255 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 412 optimal weight: 4.9990 chunk 312 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 85 HIS ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 269 GLN 7 345 ASN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 553 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 740 HIS ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS W 133 GLN W 169 GLN ** X 199 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 = 0.3961 r_free = 0.3961 target = 0.187001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.127032 restraints weight = 39823.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.127061 restraints weight = 37687.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.128919 restraints weight = 31361.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.128583 restraints weight = 23560.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.128765 restraints weight = 23698.895| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34947 Z= 0.151 Angle : 0.563 16.261 47245 Z= 0.280 Chirality : 0.042 0.186 5378 Planarity : 0.004 0.054 5947 Dihedral : 8.344 118.821 4758 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.54 % Allowed : 13.43 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4122 helix: 1.25 (0.12), residues: 1936 sheet: -0.66 (0.23), residues: 528 loop : -0.44 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 142 TYR 0.028 0.002 TYR 1 583 PHE 0.025 0.001 PHE 7 316 TRP 0.016 0.001 TRP 1 29 HIS 0.009 0.001 HIS 0 747 Details of bonding type rmsd covalent geometry : bond 0.00356 (34902) covalent geometry : angle 0.54333 (47179) hydrogen bonds : bond 0.04046 ( 1587) hydrogen bonds : angle 4.50658 ( 4491) metal coordination : bond 0.00555 ( 44) metal coordination : angle 3.93967 ( 66) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 702 time to evaluate : 1.373 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: 0 34 VAL cc_start: 0.8642 (p) cc_final: 0.8259 (m) REVERT: 0 79 ILE cc_start: 0.8323 (mt) cc_final: 0.8092 (mp) REVERT: 0 142 LYS cc_start: 0.8094 (tttt) cc_final: 0.7608 (tttp) REVERT: 0 183 LYS cc_start: 0.7530 (ttmt) cc_final: 0.7257 (mtpp) REVERT: 0 218 ILE cc_start: 0.8717 (pt) cc_final: 0.8449 (pt) REVERT: 0 236 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6686 (mt-10) REVERT: 0 270 ARG cc_start: 0.7447 (tpt-90) cc_final: 0.7087 (mmm160) REVERT: 0 357 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7547 (ttpp) REVERT: 0 365 GLN cc_start: 0.6603 (tt0) cc_final: 0.6278 (mt0) REVERT: 0 622 MET cc_start: 0.8812 (tpt) cc_final: 0.8478 (mmm) REVERT: 0 640 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7045 (mm-30) REVERT: 0 643 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6920 (ttp80) REVERT: 0 650 GLU cc_start: 0.7545 (mp0) cc_final: 0.7276 (mt-10) REVERT: 0 670 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8812 (mp) REVERT: 1 105 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6787 (mm-40) REVERT: 1 173 LYS cc_start: 0.6936 (mmtp) cc_final: 0.6566 (mmtt) REVERT: 1 178 LEU cc_start: 0.8175 (mt) cc_final: 0.7944 (tp) REVERT: 1 238 LYS cc_start: 0.7840 (pttm) cc_final: 0.7555 (tppt) REVERT: 1 318 ASP cc_start: 0.7031 (t0) cc_final: 0.6684 (t0) REVERT: 1 321 PHE cc_start: 0.7897 (m-10) cc_final: 0.7670 (m-80) REVERT: 1 346 ASP cc_start: 0.7879 (t0) cc_final: 0.7507 (t70) REVERT: 1 373 ASP cc_start: 0.7138 (t0) cc_final: 0.6801 (m-30) REVERT: 1 560 PHE cc_start: 0.8565 (m-80) cc_final: 0.8319 (m-80) REVERT: 1 628 HIS cc_start: 0.8201 (t-90) cc_final: 0.7896 (t-90) REVERT: 2 48 MET cc_start: 0.8880 (tpp) cc_final: 0.8642 (tpp) REVERT: 2 97 MET cc_start: 0.7222 (mmp) cc_final: 0.6478 (tpp) REVERT: 2 222 LEU cc_start: 0.8828 (mt) cc_final: 0.8601 (mp) REVERT: 2 224 PHE cc_start: 0.7114 (t80) cc_final: 0.6833 (t80) REVERT: 2 254 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7910 (mtt180) REVERT: 2 277 MET cc_start: 0.7156 (tpp) cc_final: 0.6908 (tpt) REVERT: 2 433 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8139 (pp) REVERT: 3 12 MET cc_start: 0.7152 (mtt) cc_final: 0.6258 (mtt) REVERT: 3 37 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7291 (ttp80) REVERT: 3 115 ASP cc_start: 0.6456 (t0) cc_final: 0.6076 (t0) REVERT: 4 51 ILE cc_start: 0.8839 (mm) cc_final: 0.8582 (mm) REVERT: 4 229 ASP cc_start: 0.7845 (t0) cc_final: 0.7587 (t70) REVERT: 4 235 TYR cc_start: 0.8889 (t80) cc_final: 0.8601 (t80) REVERT: 4 237 HIS cc_start: 0.8217 (t-170) cc_final: 0.7967 (t-90) REVERT: 5 59 SER cc_start: 0.8119 (m) cc_final: 0.7756 (p) REVERT: 6 134 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6805 (mm-30) REVERT: 6 215 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7033 (mt-10) REVERT: 6 252 ASP cc_start: 0.6976 (t0) cc_final: 0.6685 (t0) REVERT: 6 302 ASN cc_start: 0.7182 (t0) cc_final: 0.6979 (m-40) REVERT: 6 303 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7571 (tm-30) REVERT: 6 450 ASN cc_start: 0.8672 (p0) cc_final: 0.8417 (p0) REVERT: 7 179 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8255 (t) REVERT: 7 235 GLU cc_start: 0.6361 (tm-30) cc_final: 0.6019 (tm-30) REVERT: 7 236 THR cc_start: 0.7940 (p) cc_final: 0.7736 (t) REVERT: 7 381 SER cc_start: 0.8623 (m) cc_final: 0.8353 (p) REVERT: 7 404 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7484 (mmtm) REVERT: 7 454 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8504 (m) REVERT: 7 576 LYS cc_start: 0.8028 (mttt) cc_final: 0.7717 (mtmm) REVERT: 7 694 LYS cc_start: 0.7940 (tmtt) cc_final: 0.7689 (tppt) REVERT: A 15 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7457 (mttt) REVERT: A 112 LYS cc_start: 0.8071 (tttm) cc_final: 0.7458 (mtpp) REVERT: A 143 LYS cc_start: 0.7946 (tttt) cc_final: 0.7243 (mptt) REVERT: A 169 ASN cc_start: 0.8705 (m-40) cc_final: 0.8182 (m-40) REVERT: A 187 LYS cc_start: 0.7901 (pttt) cc_final: 0.7594 (pttm) REVERT: A 199 LEU cc_start: 0.8110 (tt) cc_final: 0.7874 (pp) REVERT: D 180 LEU cc_start: 0.8166 (mt) cc_final: 0.7918 (mt) REVERT: F 104 ASN cc_start: 0.8092 (t0) cc_final: 0.7456 (t0) REVERT: G 31 LEU cc_start: 0.8527 (mt) cc_final: 0.8310 (mp) REVERT: G 140 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7535 (ttmm) REVERT: W 106 VAL cc_start: 0.8062 (t) cc_final: 0.7763 (m) REVERT: W 114 ASP cc_start: 0.7882 (m-30) cc_final: 0.7536 (t0) REVERT: W 135 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7371 (mm-30) REVERT: W 145 THR cc_start: 0.6877 (p) cc_final: 0.6422 (t) REVERT: W 148 LEU cc_start: 0.6795 (mm) cc_final: 0.6269 (pp) REVERT: W 180 GLN cc_start: 0.7700 (tp40) cc_final: 0.7014 (tp40) REVERT: W 223 LYS cc_start: 0.8566 (tppt) cc_final: 0.8130 (tptp) REVERT: W 285 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6988 (mmm160) REVERT: X 203 LYS cc_start: 0.7939 (tptm) cc_final: 0.7322 (ttpt) outliers start: 97 outliers final: 62 residues processed: 754 average time/residue: 0.2344 time to fit residues: 282.3857 Evaluate side-chains 743 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 676 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 304 GLU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 670 LEU Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 432 VAL Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 407 GLN Chi-restraints excluded: chain 7 residue 158 VAL Chi-restraints excluded: chain 7 residue 179 SER Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 371 SER Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 553 GLN Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 285 ARG Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 255 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 371 optimal weight: 0.9980 chunk 260 optimal weight: 0.5980 chunk 310 optimal weight: 1.9990 chunk 367 optimal weight: 0.4980 chunk 133 optimal weight: 0.0970 chunk 327 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 692 GLN 2 85 HIS ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 GLN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 553 GLN ** 7 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 GLN ** X 199 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 = 0.3977 r_free = 0.3977 target = 0.188506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 153)---------------| | r_work = 0.3278 r_free = 0.3278 target = 0.126139 restraints weight = 39880.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.126045 restraints weight = 28933.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127478 restraints weight = 25333.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.127688 restraints weight = 22618.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.128112 restraints weight = 22601.558| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34947 Z= 0.124 Angle : 0.543 15.606 47245 Z= 0.269 Chirality : 0.041 0.189 5378 Planarity : 0.004 0.054 5947 Dihedral : 8.252 114.918 4758 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.67 % Allowed : 14.32 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.59 (0.13), residues: 4122 helix: 1.41 (0.12), residues: 1934 sheet: -0.60 (0.23), residues: 511 loop : -0.40 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 197 TYR 0.056 0.001 TYR 1 583 PHE 0.027 0.001 PHE 7 316 TRP 0.017 0.001 TRP 1 29 HIS 0.013 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00287 (34902) covalent geometry : angle 0.52462 (47179) hydrogen bonds : bond 0.03696 ( 1587) hydrogen bonds : angle 4.35782 ( 4491) metal coordination : bond 0.00438 ( 44) metal coordination : angle 3.80643 ( 66) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 693 time to evaluate : 1.140 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: 0 10 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8818 (t) REVERT: 0 34 VAL cc_start: 0.8483 (p) cc_final: 0.8126 (m) REVERT: 0 79 ILE cc_start: 0.8209 (mt) cc_final: 0.7955 (mp) REVERT: 0 90 MET cc_start: 0.8434 (mmp) cc_final: 0.7933 (mmm) REVERT: 0 96 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5432 (mp0) REVERT: 0 142 LYS cc_start: 0.7951 (tttt) cc_final: 0.7454 (tttp) REVERT: 0 183 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7199 (mtpp) REVERT: 0 218 ILE cc_start: 0.8754 (pt) cc_final: 0.8462 (pt) REVERT: 0 236 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6693 (mt-10) REVERT: 0 270 ARG cc_start: 0.7355 (tpt-90) cc_final: 0.7026 (mmm160) REVERT: 0 357 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7471 (ttpp) REVERT: 0 365 GLN cc_start: 0.6585 (tt0) cc_final: 0.6182 (mt0) REVERT: 0 622 MET cc_start: 0.8806 (tpt) cc_final: 0.8461 (mmm) REVERT: 0 640 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7064 (mm-30) REVERT: 0 643 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6892 (ttp80) REVERT: 0 650 GLU cc_start: 0.7552 (mp0) cc_final: 0.7234 (mt-10) REVERT: 1 10 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7826 (pt0) REVERT: 1 97 MET cc_start: 0.7176 (ttp) cc_final: 0.6805 (ttt) REVERT: 1 105 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6820 (mm-40) REVERT: 1 173 LYS cc_start: 0.6848 (mmtp) cc_final: 0.6435 (mmtt) REVERT: 1 178 LEU cc_start: 0.8329 (mt) cc_final: 0.7992 (tp) REVERT: 1 238 LYS cc_start: 0.7842 (pttm) cc_final: 0.7493 (tppt) REVERT: 1 318 ASP cc_start: 0.7096 (t0) cc_final: 0.6723 (t0) REVERT: 1 321 PHE cc_start: 0.7891 (m-10) cc_final: 0.7653 (m-80) REVERT: 1 346 ASP cc_start: 0.7884 (t0) cc_final: 0.7478 (t70) REVERT: 1 373 ASP cc_start: 0.7151 (t0) cc_final: 0.6784 (m-30) REVERT: 1 560 PHE cc_start: 0.8852 (m-80) cc_final: 0.8574 (m-80) REVERT: 1 628 HIS cc_start: 0.8488 (t-90) cc_final: 0.8061 (t-90) REVERT: 2 48 MET cc_start: 0.8821 (tpp) cc_final: 0.8607 (tpp) REVERT: 2 88 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7764 (pt) REVERT: 2 97 MET cc_start: 0.7442 (mmp) cc_final: 0.6634 (tpp) REVERT: 2 222 LEU cc_start: 0.8843 (mt) cc_final: 0.8617 (mt) REVERT: 2 224 PHE cc_start: 0.7272 (t80) cc_final: 0.6876 (t80) REVERT: 2 253 MET cc_start: 0.8020 (tpp) cc_final: 0.7594 (mmp) REVERT: 2 254 ARG cc_start: 0.8327 (ttm170) cc_final: 0.7876 (mtt180) REVERT: 2 277 MET cc_start: 0.7428 (tpp) cc_final: 0.6793 (tpt) REVERT: 3 12 MET cc_start: 0.7032 (mtt) cc_final: 0.6710 (mmt) REVERT: 3 37 ARG cc_start: 0.7763 (mtp-110) cc_final: 0.7233 (ttp80) REVERT: 3 115 ASP cc_start: 0.6469 (t0) cc_final: 0.6107 (t0) REVERT: 4 51 ILE cc_start: 0.8789 (mm) cc_final: 0.8543 (mm) REVERT: 4 117 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7603 (ttm170) REVERT: 4 229 ASP cc_start: 0.7946 (t0) cc_final: 0.7699 (t70) REVERT: 4 235 TYR cc_start: 0.8967 (t80) cc_final: 0.8684 (t80) REVERT: 5 59 SER cc_start: 0.7966 (m) cc_final: 0.7634 (p) REVERT: 6 134 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6816 (mm-30) REVERT: 6 215 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7000 (mt-10) REVERT: 6 252 ASP cc_start: 0.6960 (t0) cc_final: 0.6638 (t0) REVERT: 6 303 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7510 (tm-30) REVERT: 6 450 ASN cc_start: 0.8728 (p0) cc_final: 0.8442 (p0) REVERT: 7 118 PHE cc_start: 0.9001 (m-80) cc_final: 0.8779 (m-80) REVERT: 7 235 GLU cc_start: 0.6329 (tm-30) cc_final: 0.6068 (tm-30) REVERT: 7 381 SER cc_start: 0.8747 (m) cc_final: 0.8389 (p) REVERT: 7 404 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7322 (mmtm) REVERT: 7 454 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8507 (m) REVERT: 7 546 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7526 (mmtp) REVERT: 7 571 ARG cc_start: 0.7447 (ptp90) cc_final: 0.7089 (tmm-80) REVERT: 7 576 LYS cc_start: 0.8127 (mttt) cc_final: 0.7772 (mtmm) REVERT: 7 615 LEU cc_start: 0.8493 (tp) cc_final: 0.8167 (tp) REVERT: 7 694 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7687 (tppt) REVERT: A 15 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7446 (mttt) REVERT: A 112 LYS cc_start: 0.8042 (tttm) cc_final: 0.7383 (mtpp) REVERT: A 169 ASN cc_start: 0.8702 (m-40) cc_final: 0.8048 (m-40) REVERT: A 187 LYS cc_start: 0.7866 (pttt) cc_final: 0.7536 (pttm) REVERT: A 199 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7989 (pp) REVERT: D 180 LEU cc_start: 0.8057 (mt) cc_final: 0.7823 (mt) REVERT: F 103 MET cc_start: 0.7159 (mtp) cc_final: 0.6347 (mtt) REVERT: F 104 ASN cc_start: 0.8013 (t0) cc_final: 0.7355 (t0) REVERT: G 31 LEU cc_start: 0.8476 (mt) cc_final: 0.8266 (mp) REVERT: G 140 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7526 (ttmm) REVERT: W 116 ASN cc_start: 0.7521 (t0) cc_final: 0.7294 (t0) REVERT: W 135 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7347 (mm-30) REVERT: W 145 THR cc_start: 0.6778 (p) cc_final: 0.6365 (t) REVERT: W 180 GLN cc_start: 0.7572 (tp40) cc_final: 0.6918 (tp40) REVERT: W 223 LYS cc_start: 0.8647 (tppt) cc_final: 0.8216 (tmtt) REVERT: W 285 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7156 (mmm160) REVERT: X 203 LYS cc_start: 0.7940 (tptm) cc_final: 0.7227 (ttpt) outliers start: 102 outliers final: 68 residues processed: 749 average time/residue: 0.2233 time to fit residues: 268.9449 Evaluate side-chains 739 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 664 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 96 GLU Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 304 GLU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 355 ASP Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 432 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 3 residue 137 GLU Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 7 residue 158 VAL Chi-restraints excluded: chain 7 residue 340 GLU Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 371 SER Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 417 VAL Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 285 ARG Chi-restraints excluded: chain X residue 221 ILE Chi-restraints excluded: chain X residue 235 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 279 optimal weight: 0.6980 chunk 357 optimal weight: 0.5980 chunk 350 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 210 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 331 HIS ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 GLN 5 55 ASN 6 184 GLN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 553 GLN 7 596 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 116 ASN W 169 GLN W 178 GLN ** X 199 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 = 0.3970 r_free = 0.3970 target = 0.187826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 144)---------------| | r_work = 0.3284 r_free = 0.3284 target = 0.126436 restraints weight = 39802.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.125669 restraints weight = 31423.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.126886 restraints weight = 28502.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.127539 restraints weight = 25136.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.127609 restraints weight = 23130.773| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34947 Z= 0.135 Angle : 0.547 15.560 47245 Z= 0.271 Chirality : 0.041 0.196 5378 Planarity : 0.003 0.054 5947 Dihedral : 8.214 113.165 4758 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.83 % Allowed : 15.40 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.65 (0.13), residues: 4122 helix: 1.46 (0.12), residues: 1936 sheet: -0.60 (0.23), residues: 514 loop : -0.37 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 142 TYR 0.058 0.002 TYR 1 583 PHE 0.034 0.001 PHE X 259 TRP 0.017 0.001 TRP 1 29 HIS 0.012 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00319 (34902) covalent geometry : angle 0.52934 (47179) hydrogen bonds : bond 0.03669 ( 1587) hydrogen bonds : angle 4.31774 ( 4491) metal coordination : bond 0.00477 ( 44) metal coordination : angle 3.69010 ( 66) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 684 time to evaluate : 1.349 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: 0 34 VAL cc_start: 0.8415 (p) cc_final: 0.8033 (m) REVERT: 0 79 ILE cc_start: 0.8289 (mt) cc_final: 0.8040 (mp) REVERT: 0 90 MET cc_start: 0.8458 (mmp) cc_final: 0.8041 (mmm) REVERT: 0 96 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5501 (mp0) REVERT: 0 101 GLU cc_start: 0.7351 (pt0) cc_final: 0.6914 (pm20) REVERT: 0 142 LYS cc_start: 0.8012 (tttt) cc_final: 0.7513 (tttp) REVERT: 0 176 PHE cc_start: 0.8016 (m-80) cc_final: 0.7658 (m-80) REVERT: 0 183 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7249 (mtpp) REVERT: 0 218 ILE cc_start: 0.8760 (pt) cc_final: 0.8471 (pt) REVERT: 0 236 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6831 (mt-10) REVERT: 0 270 ARG cc_start: 0.7365 (tpt-90) cc_final: 0.7032 (mmm160) REVERT: 0 357 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7483 (ttpp) REVERT: 0 365 GLN cc_start: 0.6568 (tt0) cc_final: 0.6123 (mt0) REVERT: 0 622 MET cc_start: 0.8842 (tpt) cc_final: 0.8468 (mmm) REVERT: 0 640 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7101 (mm-30) REVERT: 0 643 ARG cc_start: 0.7320 (ttp80) cc_final: 0.6904 (ttp80) REVERT: 0 650 GLU cc_start: 0.7572 (mp0) cc_final: 0.7239 (mt-10) REVERT: 1 10 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7506 (pt0) REVERT: 1 105 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6786 (mm-40) REVERT: 1 173 LYS cc_start: 0.6866 (mmtp) cc_final: 0.6465 (mmtt) REVERT: 1 178 LEU cc_start: 0.8306 (mt) cc_final: 0.7999 (tp) REVERT: 1 238 LYS cc_start: 0.7831 (pttm) cc_final: 0.7512 (tppt) REVERT: 1 302 MET cc_start: 0.5834 (tpp) cc_final: 0.4800 (tpt) REVERT: 1 318 ASP cc_start: 0.7126 (t0) cc_final: 0.6763 (t0) REVERT: 1 321 PHE cc_start: 0.7894 (m-10) cc_final: 0.7681 (m-80) REVERT: 1 346 ASP cc_start: 0.8075 (t0) cc_final: 0.7667 (t70) REVERT: 1 373 ASP cc_start: 0.7071 (t0) cc_final: 0.6747 (m-30) REVERT: 1 437 LEU cc_start: 0.8622 (tp) cc_final: 0.8312 (pp) REVERT: 1 560 PHE cc_start: 0.8763 (m-80) cc_final: 0.8511 (m-80) REVERT: 1 628 HIS cc_start: 0.8377 (t-90) cc_final: 0.7951 (t-90) REVERT: 2 88 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7792 (pt) REVERT: 2 97 MET cc_start: 0.7407 (mmp) cc_final: 0.6698 (tpp) REVERT: 2 165 ASN cc_start: 0.8236 (t0) cc_final: 0.7934 (p0) REVERT: 2 222 LEU cc_start: 0.8818 (mt) cc_final: 0.8601 (mt) REVERT: 2 227 MET cc_start: 0.7349 (ttp) cc_final: 0.6923 (ptt) REVERT: 2 253 MET cc_start: 0.7950 (tpp) cc_final: 0.7606 (mmp) REVERT: 2 254 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7828 (mtt180) REVERT: 2 277 MET cc_start: 0.7390 (tpp) cc_final: 0.6788 (tpt) REVERT: 3 12 MET cc_start: 0.6627 (mtt) cc_final: 0.6018 (mtt) REVERT: 3 19 ASP cc_start: 0.7811 (m-30) cc_final: 0.7497 (m-30) REVERT: 3 37 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7284 (ttp80) REVERT: 3 56 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: 3 115 ASP cc_start: 0.6477 (t0) cc_final: 0.6099 (t0) REVERT: 3 129 THR cc_start: 0.8448 (m) cc_final: 0.7844 (t) REVERT: 4 229 ASP cc_start: 0.7929 (t0) cc_final: 0.7673 (t70) REVERT: 4 235 TYR cc_start: 0.8944 (t80) cc_final: 0.8677 (t80) REVERT: 4 237 HIS cc_start: 0.8259 (t-170) cc_final: 0.8024 (t-90) REVERT: 5 59 SER cc_start: 0.8024 (m) cc_final: 0.7704 (p) REVERT: 6 134 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6872 (mm-30) REVERT: 6 215 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7021 (mt-10) REVERT: 6 252 ASP cc_start: 0.6975 (t0) cc_final: 0.6657 (t0) REVERT: 6 303 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7508 (tm-30) REVERT: 6 450 ASN cc_start: 0.8711 (p0) cc_final: 0.8405 (p0) REVERT: 7 118 PHE cc_start: 0.8975 (m-80) cc_final: 0.8773 (m-80) REVERT: 7 381 SER cc_start: 0.8757 (m) cc_final: 0.8414 (p) REVERT: 7 404 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7417 (mmtm) REVERT: 7 454 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8427 (m) REVERT: 7 546 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7511 (mmtp) REVERT: 7 571 ARG cc_start: 0.7411 (ptp90) cc_final: 0.7068 (tmm-80) REVERT: 7 576 LYS cc_start: 0.8136 (mttt) cc_final: 0.7732 (mtmm) REVERT: 7 615 LEU cc_start: 0.8575 (tp) cc_final: 0.8242 (tp) REVERT: 7 694 LYS cc_start: 0.7971 (tmtt) cc_final: 0.7688 (tppt) REVERT: 7 722 ARG cc_start: 0.7825 (ttp-110) cc_final: 0.7201 (ptm-80) REVERT: A 15 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7448 (mttt) REVERT: A 112 LYS cc_start: 0.8072 (tttm) cc_final: 0.7474 (mtpp) REVERT: A 143 LYS cc_start: 0.7686 (ttmt) cc_final: 0.6834 (mptt) REVERT: A 169 ASN cc_start: 0.8703 (m-40) cc_final: 0.8077 (m-40) REVERT: A 187 LYS cc_start: 0.7882 (pttt) cc_final: 0.7564 (pttm) REVERT: A 199 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8025 (pp) REVERT: D 180 LEU cc_start: 0.8070 (mt) cc_final: 0.7839 (mt) REVERT: F 103 MET cc_start: 0.7213 (mtp) cc_final: 0.6422 (mtt) REVERT: F 104 ASN cc_start: 0.8202 (t0) cc_final: 0.7522 (t0) REVERT: G 31 LEU cc_start: 0.8498 (mt) cc_final: 0.8280 (mp) REVERT: G 140 LYS cc_start: 0.7875 (ttpp) cc_final: 0.7539 (ttmm) REVERT: W 116 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7309 (t0) REVERT: W 135 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7327 (mm-30) REVERT: W 180 GLN cc_start: 0.7497 (tp40) cc_final: 0.6305 (tp40) REVERT: W 184 ASP cc_start: 0.7759 (m-30) cc_final: 0.7073 (m-30) REVERT: W 223 LYS cc_start: 0.8641 (tppt) cc_final: 0.8240 (tmtt) REVERT: W 285 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7169 (mmm160) REVERT: X 203 LYS cc_start: 0.8018 (tptm) cc_final: 0.7245 (ttpt) REVERT: X 259 PHE cc_start: 0.7433 (m-10) cc_final: 0.7225 (m-10) outliers start: 108 outliers final: 80 residues processed: 738 average time/residue: 0.2319 time to fit residues: 274.0304 Evaluate side-chains 750 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 663 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 96 GLU Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 235 ASP Chi-restraints excluded: chain 0 residue 304 GLU Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 355 ASP Chi-restraints excluded: chain 1 residue 427 SER Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 163 VAL Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 3 residue 137 GLU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 7 residue 158 VAL Chi-restraints excluded: chain 7 residue 160 ILE Chi-restraints excluded: chain 7 residue 236 THR Chi-restraints excluded: chain 7 residue 371 SER Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 417 VAL Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 659 ASP Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 116 ASN Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 285 ARG Chi-restraints excluded: chain X residue 235 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 380 optimal weight: 0.6980 chunk 396 optimal weight: 0.9980 chunk 411 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 326 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 85 HIS ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 GLN 6 184 GLN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 GLN W 178 GLN ** X 199 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 = 0.3970 r_free = 0.3970 target = 0.187906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.127506 restraints weight = 39891.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.128328 restraints weight = 35995.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.129793 restraints weight = 28898.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.130035 restraints weight = 23008.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.130061 restraints weight = 23277.421| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34947 Z= 0.145 Angle : 0.558 16.032 47245 Z= 0.276 Chirality : 0.042 0.198 5378 Planarity : 0.003 0.054 5947 Dihedral : 8.204 111.572 4758 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.85 % Allowed : 15.84 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.67 (0.13), residues: 4122 helix: 1.47 (0.12), residues: 1937 sheet: -0.56 (0.23), residues: 514 loop : -0.36 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 142 TYR 0.050 0.001 TYR 1 583 PHE 0.033 0.001 PHE 2 224 TRP 0.018 0.001 TRP 1 29 HIS 0.010 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00345 (34902) covalent geometry : angle 0.54140 (47179) hydrogen bonds : bond 0.03677 ( 1587) hydrogen bonds : angle 4.29712 ( 4491) metal coordination : bond 0.00496 ( 44) metal coordination : angle 3.66083 ( 66) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 683 time to evaluate : 1.448 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: 0 34 VAL cc_start: 0.8676 (p) cc_final: 0.8308 (m) REVERT: 0 79 ILE cc_start: 0.8326 (mt) cc_final: 0.8104 (mp) REVERT: 0 96 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5428 (mp0) REVERT: 0 176 PHE cc_start: 0.7979 (m-80) cc_final: 0.7606 (m-80) REVERT: 0 183 LYS cc_start: 0.7574 (ttmt) cc_final: 0.7333 (mtpp) REVERT: 0 218 ILE cc_start: 0.8815 (pt) cc_final: 0.8518 (pt) REVERT: 0 236 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6855 (mt-10) REVERT: 0 270 ARG cc_start: 0.7418 (tpt-90) cc_final: 0.6925 (tpt90) REVERT: 0 365 GLN cc_start: 0.6569 (tt0) cc_final: 0.6122 (mt0) REVERT: 0 622 MET cc_start: 0.8856 (tpt) cc_final: 0.8514 (mmm) REVERT: 0 643 ARG cc_start: 0.7394 (ttp80) cc_final: 0.7086 (ttp80) REVERT: 0 650 GLU cc_start: 0.7564 (mp0) cc_final: 0.7301 (mt-10) REVERT: 1 10 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7450 (pt0) REVERT: 1 97 MET cc_start: 0.7110 (ttp) cc_final: 0.6684 (ttt) REVERT: 1 105 GLN cc_start: 0.7356 (mm-40) cc_final: 0.6918 (mm-40) REVERT: 1 173 LYS cc_start: 0.6846 (mmtp) cc_final: 0.6504 (mmtt) REVERT: 1 178 LEU cc_start: 0.8212 (mt) cc_final: 0.7963 (tp) REVERT: 1 238 LYS cc_start: 0.7784 (pttm) cc_final: 0.7566 (tppt) REVERT: 1 318 ASP cc_start: 0.7112 (t0) cc_final: 0.6770 (t0) REVERT: 1 321 PHE cc_start: 0.7883 (m-10) cc_final: 0.7656 (m-80) REVERT: 1 346 ASP cc_start: 0.8072 (t0) cc_final: 0.7672 (t70) REVERT: 1 373 ASP cc_start: 0.7057 (t0) cc_final: 0.6756 (m-30) REVERT: 1 437 LEU cc_start: 0.8513 (tp) cc_final: 0.8227 (pp) REVERT: 1 560 PHE cc_start: 0.8582 (m-80) cc_final: 0.8381 (m-80) REVERT: 1 628 HIS cc_start: 0.8182 (t-90) cc_final: 0.7798 (t-90) REVERT: 1 633 TYR cc_start: 0.7739 (t80) cc_final: 0.7117 (t80) REVERT: 2 13 TYR cc_start: 0.8424 (t80) cc_final: 0.8044 (t80) REVERT: 2 88 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7856 (pt) REVERT: 2 97 MET cc_start: 0.7242 (mmp) cc_final: 0.6795 (mmp) REVERT: 2 222 LEU cc_start: 0.8751 (mt) cc_final: 0.8544 (mt) REVERT: 2 227 MET cc_start: 0.7107 (ttp) cc_final: 0.6747 (ptm) REVERT: 2 277 MET cc_start: 0.7331 (tpp) cc_final: 0.6842 (tpt) REVERT: 3 19 ASP cc_start: 0.7778 (m-30) cc_final: 0.7161 (m-30) REVERT: 3 37 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7275 (ttp80) REVERT: 3 56 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: 3 115 ASP cc_start: 0.6469 (t0) cc_final: 0.6106 (t0) REVERT: 3 120 LEU cc_start: 0.8330 (mt) cc_final: 0.7999 (mt) REVERT: 4 229 ASP cc_start: 0.7863 (t0) cc_final: 0.7604 (t70) REVERT: 4 235 TYR cc_start: 0.8900 (t80) cc_final: 0.8652 (t80) REVERT: 4 237 HIS cc_start: 0.8268 (t-170) cc_final: 0.8033 (t-90) REVERT: 5 59 SER cc_start: 0.8133 (m) cc_final: 0.7794 (p) REVERT: 6 134 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6837 (mm-30) REVERT: 6 215 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7034 (mt-10) REVERT: 6 252 ASP cc_start: 0.6943 (t0) cc_final: 0.6633 (t0) REVERT: 6 303 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7467 (tm-30) REVERT: 6 450 ASN cc_start: 0.8643 (p0) cc_final: 0.8357 (p0) REVERT: 7 381 SER cc_start: 0.8801 (m) cc_final: 0.8415 (p) REVERT: 7 404 LYS cc_start: 0.8370 (mmmm) cc_final: 0.7507 (mmtm) REVERT: 7 454 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8371 (m) REVERT: 7 546 LYS cc_start: 0.7808 (mmtp) cc_final: 0.7558 (mmtp) REVERT: 7 571 ARG cc_start: 0.7366 (ptp90) cc_final: 0.7062 (tmm-80) REVERT: 7 576 LYS cc_start: 0.8086 (mttt) cc_final: 0.7724 (mtmm) REVERT: 7 615 LEU cc_start: 0.8590 (tp) cc_final: 0.8259 (tp) REVERT: 7 694 LYS cc_start: 0.7946 (tmtt) cc_final: 0.7691 (tppt) REVERT: 7 722 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7247 (mtp-110) REVERT: A 15 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7493 (mttt) REVERT: A 112 LYS cc_start: 0.8082 (tttm) cc_final: 0.7517 (mtpp) REVERT: A 143 LYS cc_start: 0.7748 (ttmt) cc_final: 0.6937 (mptt) REVERT: A 169 ASN cc_start: 0.8705 (m-40) cc_final: 0.8303 (m110) REVERT: A 187 LYS cc_start: 0.7880 (pttt) cc_final: 0.7571 (pttm) REVERT: A 1454 MET cc_start: 0.6126 (mmm) cc_final: 0.5586 (mmm) REVERT: D 130 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6187 (mt) REVERT: D 180 LEU cc_start: 0.8106 (mt) cc_final: 0.7880 (mt) REVERT: F 104 ASN cc_start: 0.8280 (t0) cc_final: 0.7664 (t0) REVERT: G 31 LEU cc_start: 0.8525 (mt) cc_final: 0.8311 (mp) REVERT: G 140 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7545 (ttmm) REVERT: W 135 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7334 (mm-30) REVERT: W 156 LEU cc_start: 0.8384 (mm) cc_final: 0.8103 (mt) REVERT: W 180 GLN cc_start: 0.7562 (tp40) cc_final: 0.6336 (tp40) REVERT: W 184 ASP cc_start: 0.7696 (m-30) cc_final: 0.7028 (m-30) REVERT: W 223 LYS cc_start: 0.8573 (tppt) cc_final: 0.8269 (tmtt) REVERT: W 229 ARG cc_start: 0.6848 (mtt90) cc_final: 0.6626 (mpt180) REVERT: W 285 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7105 (mmm160) REVERT: X 203 LYS cc_start: 0.8023 (tptm) cc_final: 0.7252 (ttpt) outliers start: 109 outliers final: 89 residues processed: 743 average time/residue: 0.2299 time to fit residues: 273.1388 Evaluate side-chains 757 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 662 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 96 GLU Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 235 ASP Chi-restraints excluded: chain 0 residue 304 GLU Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 440 LEU Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 675 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 355 ASP Chi-restraints excluded: chain 1 residue 427 SER Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 163 VAL Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 7 residue 122 ARG Chi-restraints excluded: chain 7 residue 158 VAL Chi-restraints excluded: chain 7 residue 160 ILE Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 371 SER Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 417 VAL Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 659 ASP Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 679 SER Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 740 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 175 LEU Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 285 ARG Chi-restraints excluded: chain X residue 235 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 175 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 322 optimal weight: 0.5980 chunk 346 optimal weight: 1.9990 chunk 354 optimal weight: 0.1980 chunk 407 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 271 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 85 HIS ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 GLN 6 184 GLN ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 ASN W 169 GLN ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.188393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124018 restraints weight = 40137.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.123321 restraints weight = 26547.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.125663 restraints weight = 21590.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.126325 restraints weight = 18728.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.126414 restraints weight = 18417.637| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34947 Z= 0.127 Angle : 0.553 15.459 47245 Z= 0.273 Chirality : 0.041 0.167 5378 Planarity : 0.003 0.054 5947 Dihedral : 8.182 109.610 4758 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.72 % Allowed : 16.21 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.75 (0.13), residues: 4122 helix: 1.55 (0.12), residues: 1934 sheet: -0.53 (0.23), residues: 512 loop : -0.33 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 142 TYR 0.071 0.001 TYR 1 583 PHE 0.036 0.001 PHE X 259 TRP 0.020 0.001 TRP 1 29 HIS 0.010 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00299 (34902) covalent geometry : angle 0.53595 (47179) hydrogen bonds : bond 0.03533 ( 1587) hydrogen bonds : angle 4.24328 ( 4491) metal coordination : bond 0.00449 ( 44) metal coordination : angle 3.64148 ( 66) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 668 time to evaluate : 1.348 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: 0 34 VAL cc_start: 0.8556 (p) cc_final: 0.8180 (m) REVERT: 0 79 ILE cc_start: 0.8250 (mt) cc_final: 0.8008 (mp) REVERT: 0 96 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5386 (mp0) REVERT: 0 142 LYS cc_start: 0.7900 (tttt) cc_final: 0.7426 (tttp) REVERT: 0 176 PHE cc_start: 0.8032 (m-80) cc_final: 0.7676 (m-80) REVERT: 0 183 LYS cc_start: 0.7567 (ttmt) cc_final: 0.7298 (mtpp) REVERT: 0 218 ILE cc_start: 0.8839 (pt) cc_final: 0.8553 (pt) REVERT: 0 236 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6810 (mt-10) REVERT: 0 270 ARG cc_start: 0.7317 (tpt-90) cc_final: 0.6777 (tpt90) REVERT: 0 365 GLN cc_start: 0.6555 (tt0) cc_final: 0.6113 (mt0) REVERT: 0 622 MET cc_start: 0.8856 (tpt) cc_final: 0.8505 (mmm) REVERT: 0 643 ARG cc_start: 0.7348 (ttp80) cc_final: 0.6935 (ttp80) REVERT: 0 650 GLU cc_start: 0.7574 (mp0) cc_final: 0.7302 (mt-10) REVERT: 1 10 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7492 (pt0) REVERT: 1 105 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6841 (mm-40) REVERT: 1 173 LYS cc_start: 0.6803 (mmtp) cc_final: 0.6361 (mmtt) REVERT: 1 178 LEU cc_start: 0.8404 (mt) cc_final: 0.8006 (tp) REVERT: 1 238 LYS cc_start: 0.7806 (pttm) cc_final: 0.7495 (tppt) REVERT: 1 318 ASP cc_start: 0.7198 (t0) cc_final: 0.6839 (t0) REVERT: 1 321 PHE cc_start: 0.7885 (m-10) cc_final: 0.7605 (m-80) REVERT: 1 346 ASP cc_start: 0.8084 (t0) cc_final: 0.7730 (t70) REVERT: 1 373 ASP cc_start: 0.7122 (t0) cc_final: 0.6765 (m-30) REVERT: 1 437 LEU cc_start: 0.8702 (tp) cc_final: 0.8374 (pp) REVERT: 1 560 PHE cc_start: 0.8941 (m-80) cc_final: 0.8714 (m-80) REVERT: 1 628 HIS cc_start: 0.8516 (t-90) cc_final: 0.8037 (t-90) REVERT: 2 13 TYR cc_start: 0.8425 (t80) cc_final: 0.8080 (t80) REVERT: 2 88 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7630 (pt) REVERT: 2 97 MET cc_start: 0.7481 (mmp) cc_final: 0.6836 (mmp) REVERT: 2 227 MET cc_start: 0.7638 (ttp) cc_final: 0.6854 (ptm) REVERT: 2 277 MET cc_start: 0.7364 (tpp) cc_final: 0.6738 (tpt) REVERT: 3 12 MET cc_start: 0.7148 (tpp) cc_final: 0.6901 (tpp) REVERT: 3 37 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7440 (mtp-110) REVERT: 3 56 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: 3 115 ASP cc_start: 0.6538 (t0) cc_final: 0.6179 (t0) REVERT: 4 81 GLN cc_start: 0.8851 (mm110) cc_final: 0.8518 (mm-40) REVERT: 4 229 ASP cc_start: 0.8010 (t0) cc_final: 0.7760 (t70) REVERT: 4 235 TYR cc_start: 0.9000 (t80) cc_final: 0.8701 (t80) REVERT: 4 237 HIS cc_start: 0.8300 (t-170) cc_final: 0.8063 (t-90) REVERT: 4 281 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7522 (mtm-85) REVERT: 5 59 SER cc_start: 0.7952 (m) cc_final: 0.7650 (p) REVERT: 6 134 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6851 (mm-30) REVERT: 6 215 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6989 (mt-10) REVERT: 6 252 ASP cc_start: 0.6963 (t0) cc_final: 0.6639 (t0) REVERT: 6 303 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7457 (tm-30) REVERT: 6 450 ASN cc_start: 0.8748 (p0) cc_final: 0.8461 (p0) REVERT: 7 122 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7387 (tmt170) REVERT: 7 220 TYR cc_start: 0.6225 (t80) cc_final: 0.5994 (t80) REVERT: 7 235 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6075 (mt-10) REVERT: 7 349 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8180 (t0) REVERT: 7 381 SER cc_start: 0.8847 (m) cc_final: 0.8436 (p) REVERT: 7 404 LYS cc_start: 0.8351 (mmmm) cc_final: 0.7447 (mmtm) REVERT: 7 454 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8367 (m) REVERT: 7 546 LYS cc_start: 0.7772 (mmtp) cc_final: 0.7520 (mmtp) REVERT: 7 571 ARG cc_start: 0.7521 (ptp90) cc_final: 0.7100 (tmm-80) REVERT: 7 576 LYS cc_start: 0.8162 (mttt) cc_final: 0.7756 (mtmm) REVERT: 7 615 LEU cc_start: 0.8568 (tp) cc_final: 0.8251 (tp) REVERT: 7 694 LYS cc_start: 0.8002 (tmtt) cc_final: 0.7674 (tppt) REVERT: 7 722 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7256 (mtp-110) REVERT: A 15 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7434 (mttt) REVERT: A 112 LYS cc_start: 0.8022 (tttm) cc_final: 0.7420 (mtpp) REVERT: A 143 LYS cc_start: 0.7683 (ttmt) cc_final: 0.6795 (mptt) REVERT: A 169 ASN cc_start: 0.8694 (m-40) cc_final: 0.8129 (m110) REVERT: A 187 LYS cc_start: 0.7828 (pttt) cc_final: 0.7505 (pttm) REVERT: A 1454 MET cc_start: 0.6060 (mmm) cc_final: 0.5062 (mmt) REVERT: D 130 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6093 (mt) REVERT: D 180 LEU cc_start: 0.8052 (mt) cc_final: 0.7841 (mt) REVERT: F 103 MET cc_start: 0.7266 (mtp) cc_final: 0.6435 (mtt) REVERT: F 104 ASN cc_start: 0.8318 (t0) cc_final: 0.7677 (t0) REVERT: G 140 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7648 (ttmm) REVERT: W 135 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7320 (mm-30) REVERT: W 146 GLU cc_start: 0.7296 (mp0) cc_final: 0.6856 (mp0) REVERT: W 180 GLN cc_start: 0.7394 (tp40) cc_final: 0.6181 (tp40) REVERT: W 184 ASP cc_start: 0.7847 (m-30) cc_final: 0.7119 (m-30) REVERT: W 223 LYS cc_start: 0.8691 (tppt) cc_final: 0.8210 (tmtt) REVERT: W 285 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7267 (mmm160) REVERT: X 203 LYS cc_start: 0.7986 (tptm) cc_final: 0.7127 (ttpt) REVERT: X 211 LYS cc_start: 0.7578 (mttp) cc_final: 0.7218 (mtmt) outliers start: 104 outliers final: 82 residues processed: 727 average time/residue: 0.2274 time to fit residues: 265.7737 Evaluate side-chains 736 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 646 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 96 GLU Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 235 ASP Chi-restraints excluded: chain 0 residue 304 GLU Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 440 LEU Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 355 ASP Chi-restraints excluded: chain 1 residue 427 SER Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 163 VAL Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 7 residue 122 ARG Chi-restraints excluded: chain 7 residue 160 ILE Chi-restraints excluded: chain 7 residue 245 LEU Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 349 ASN Chi-restraints excluded: chain 7 residue 371 SER Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 417 VAL Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 659 ASP Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 679 SER Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 740 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 285 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 294 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 383 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 263 HIS ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 GLN ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.187086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.123477 restraints weight = 40115.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.124050 restraints weight = 26446.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.123048 restraints weight = 21893.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.123810 restraints weight = 23281.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.124101 restraints weight = 20346.157| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34947 Z= 0.156 Angle : 0.581 16.026 47245 Z= 0.285 Chirality : 0.042 0.167 5378 Planarity : 0.004 0.054 5947 Dihedral : 8.203 107.881 4758 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.54 % Allowed : 16.71 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.75 (0.13), residues: 4122 helix: 1.51 (0.12), residues: 1937 sheet: -0.47 (0.23), residues: 519 loop : -0.30 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 197 TYR 0.063 0.002 TYR 1 583 PHE 0.035 0.001 PHE 2 224 TRP 0.020 0.001 TRP 1 29 HIS 0.010 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00376 (34902) covalent geometry : angle 0.56423 (47179) hydrogen bonds : bond 0.03685 ( 1587) hydrogen bonds : angle 4.25835 ( 4491) metal coordination : bond 0.00615 ( 44) metal coordination : angle 3.80416 ( 66) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 667 time to evaluate : 1.319 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: 0 34 VAL cc_start: 0.8650 (p) cc_final: 0.8273 (m) REVERT: 0 61 MET cc_start: 0.7919 (mmm) cc_final: 0.7677 (mtp) REVERT: 0 79 ILE cc_start: 0.8258 (mt) cc_final: 0.8015 (mp) REVERT: 0 96 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5247 (mp0) REVERT: 0 142 LYS cc_start: 0.7857 (tttt) cc_final: 0.7410 (tttp) REVERT: 0 176 PHE cc_start: 0.8066 (m-80) cc_final: 0.7702 (m-80) REVERT: 0 183 LYS cc_start: 0.7542 (ttmt) cc_final: 0.7264 (mtpp) REVERT: 0 218 ILE cc_start: 0.8854 (pt) cc_final: 0.8598 (pt) REVERT: 0 236 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6809 (mt-10) REVERT: 0 270 ARG cc_start: 0.7334 (tpt-90) cc_final: 0.6782 (tpt90) REVERT: 0 365 GLN cc_start: 0.6593 (tt0) cc_final: 0.6119 (mt0) REVERT: 0 622 MET cc_start: 0.8918 (tpt) cc_final: 0.8578 (mmm) REVERT: 0 643 ARG cc_start: 0.7344 (ttp80) cc_final: 0.7058 (ttp80) REVERT: 0 650 GLU cc_start: 0.7607 (mp0) cc_final: 0.7348 (mt-10) REVERT: 1 105 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6822 (mm-40) REVERT: 1 173 LYS cc_start: 0.6859 (mmtp) cc_final: 0.6376 (mmtt) REVERT: 1 178 LEU cc_start: 0.8441 (mt) cc_final: 0.7997 (tp) REVERT: 1 238 LYS cc_start: 0.7845 (pttm) cc_final: 0.7483 (tppt) REVERT: 1 318 ASP cc_start: 0.7241 (t0) cc_final: 0.6892 (t0) REVERT: 1 321 PHE cc_start: 0.7884 (m-10) cc_final: 0.7600 (m-80) REVERT: 1 346 ASP cc_start: 0.8084 (t0) cc_final: 0.7700 (t70) REVERT: 1 373 ASP cc_start: 0.7092 (t0) cc_final: 0.6723 (m-30) REVERT: 1 437 LEU cc_start: 0.8791 (tp) cc_final: 0.8463 (pp) REVERT: 1 628 HIS cc_start: 0.8505 (t-90) cc_final: 0.8024 (t-90) REVERT: 2 13 TYR cc_start: 0.8410 (t80) cc_final: 0.8060 (t80) REVERT: 2 38 ILE cc_start: 0.8809 (tp) cc_final: 0.8541 (tp) REVERT: 2 48 MET cc_start: 0.8705 (tpp) cc_final: 0.8356 (tpt) REVERT: 2 88 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7627 (pt) REVERT: 2 227 MET cc_start: 0.7728 (ttp) cc_final: 0.6886 (ptm) REVERT: 2 428 GLU cc_start: 0.7211 (mp0) cc_final: 0.6837 (mp0) REVERT: 3 12 MET cc_start: 0.6999 (tpp) cc_final: 0.6782 (tpp) REVERT: 3 37 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7443 (mtp-110) REVERT: 3 56 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6102 (m-80) REVERT: 3 115 ASP cc_start: 0.6473 (t0) cc_final: 0.6104 (t0) REVERT: 4 229 ASP cc_start: 0.8053 (t0) cc_final: 0.7807 (t70) REVERT: 4 235 TYR cc_start: 0.9047 (t80) cc_final: 0.8735 (t80) REVERT: 4 281 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7877 (mtm-85) REVERT: 4 323 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8318 (tptp) REVERT: 5 59 SER cc_start: 0.7785 (m) cc_final: 0.7519 (p) REVERT: 6 134 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6898 (mm-30) REVERT: 6 215 GLU cc_start: 0.7735 (mm-30) cc_final: 0.6992 (mt-10) REVERT: 6 252 ASP cc_start: 0.6984 (t0) cc_final: 0.6661 (t0) REVERT: 6 294 GLU cc_start: 0.6851 (tt0) cc_final: 0.6476 (mt-10) REVERT: 6 303 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7477 (tm-30) REVERT: 6 450 ASN cc_start: 0.8778 (p0) cc_final: 0.8477 (p0) REVERT: 7 124 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.6824 (ttm-80) REVERT: 7 220 TYR cc_start: 0.6325 (t80) cc_final: 0.6032 (t80) REVERT: 7 235 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6198 (mt-10) REVERT: 7 329 ARG cc_start: 0.7478 (mmm-85) cc_final: 0.6976 (mmm-85) REVERT: 7 349 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8240 (t0) REVERT: 7 381 SER cc_start: 0.8892 (m) cc_final: 0.8491 (p) REVERT: 7 404 LYS cc_start: 0.8350 (mmmm) cc_final: 0.7508 (mmtm) REVERT: 7 454 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8340 (m) REVERT: 7 546 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7543 (mmtp) REVERT: 7 571 ARG cc_start: 0.7567 (ptp90) cc_final: 0.7098 (tmm-80) REVERT: 7 576 LYS cc_start: 0.8234 (mttt) cc_final: 0.7803 (mtmm) REVERT: 7 615 LEU cc_start: 0.8589 (tp) cc_final: 0.8265 (tp) REVERT: 7 694 LYS cc_start: 0.7949 (tmtt) cc_final: 0.7621 (tppt) REVERT: A 15 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7425 (mttt) REVERT: A 112 LYS cc_start: 0.8010 (tttm) cc_final: 0.7395 (mtpp) REVERT: A 143 LYS cc_start: 0.7662 (ttmt) cc_final: 0.6744 (mptt) REVERT: A 169 ASN cc_start: 0.8738 (m-40) cc_final: 0.8152 (m110) REVERT: A 187 LYS cc_start: 0.7827 (pttt) cc_final: 0.7508 (pttm) REVERT: A 1454 MET cc_start: 0.6081 (mmm) cc_final: 0.5078 (mmt) REVERT: B 1178 ASN cc_start: 0.8103 (t0) cc_final: 0.7377 (t0) REVERT: D 130 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6104 (mt) REVERT: D 180 LEU cc_start: 0.8134 (mt) cc_final: 0.7933 (mt) REVERT: F 103 MET cc_start: 0.7312 (mtp) cc_final: 0.6465 (mtt) REVERT: F 104 ASN cc_start: 0.8412 (t0) cc_final: 0.7765 (t0) REVERT: G 140 LYS cc_start: 0.7980 (ttpp) cc_final: 0.7667 (ttmm) REVERT: W 135 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7339 (mm-30) REVERT: W 146 GLU cc_start: 0.7350 (mp0) cc_final: 0.7044 (mp0) REVERT: W 180 GLN cc_start: 0.7333 (tp40) cc_final: 0.6067 (tp40) REVERT: W 184 ASP cc_start: 0.7865 (m-30) cc_final: 0.7107 (m-30) REVERT: W 223 LYS cc_start: 0.8728 (tppt) cc_final: 0.8153 (tmtt) REVERT: W 285 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7264 (mmm160) REVERT: X 203 LYS cc_start: 0.8060 (tptm) cc_final: 0.7195 (ttpt) REVERT: X 211 LYS cc_start: 0.7592 (mttp) cc_final: 0.7208 (mtmt) outliers start: 97 outliers final: 82 residues processed: 725 average time/residue: 0.2319 time to fit residues: 270.5824 Evaluate side-chains 750 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 661 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 96 GLU Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 235 ASP Chi-restraints excluded: chain 0 residue 304 GLU Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 440 LEU Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 675 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 355 ASP Chi-restraints excluded: chain 1 residue 427 SER Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 7 residue 158 VAL Chi-restraints excluded: chain 7 residue 160 ILE Chi-restraints excluded: chain 7 residue 245 LEU Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 349 ASN Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 417 VAL Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 659 ASP Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 679 SER Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 740 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 285 ARG Chi-restraints excluded: chain X residue 235 THR Chi-restraints excluded: chain X residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 395 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 368 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 GLN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN 7 376 ASN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 GLN ** X 199 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 = 0.3971 r_free = 0.3971 target = 0.187645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122885 restraints weight = 40342.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.123323 restraints weight = 25825.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.123814 restraints weight = 21227.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.124961 restraints weight = 20476.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125313 restraints weight = 18376.972| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34947 Z= 0.147 Angle : 0.580 15.820 47245 Z= 0.285 Chirality : 0.042 0.168 5378 Planarity : 0.004 0.055 5947 Dihedral : 8.197 105.254 4758 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.38 % Allowed : 17.12 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.78 (0.13), residues: 4122 helix: 1.53 (0.12), residues: 1936 sheet: -0.45 (0.23), residues: 519 loop : -0.28 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 4 146 TYR 0.054 0.001 TYR 1 583 PHE 0.029 0.001 PHE 7 316 TRP 0.022 0.001 TRP 1 29 HIS 0.010 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00352 (34902) covalent geometry : angle 0.56349 (47179) hydrogen bonds : bond 0.03615 ( 1587) hydrogen bonds : angle 4.24366 ( 4491) metal coordination : bond 0.00576 ( 44) metal coordination : angle 3.67435 ( 66) Misc. bond : bond 0.00051 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 663 time to evaluate : 1.306 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: 0 34 VAL cc_start: 0.8658 (p) cc_final: 0.8281 (m) REVERT: 0 59 TYR cc_start: 0.8550 (t80) cc_final: 0.8148 (t80) REVERT: 0 79 ILE cc_start: 0.8266 (mt) cc_final: 0.8013 (mp) REVERT: 0 90 MET cc_start: 0.8508 (mmp) cc_final: 0.8087 (mmm) REVERT: 0 96 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5257 (mp0) REVERT: 0 142 LYS cc_start: 0.7925 (tttt) cc_final: 0.7453 (tttp) REVERT: 0 176 PHE cc_start: 0.8056 (m-80) cc_final: 0.7675 (m-80) REVERT: 0 183 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7279 (mtpp) REVERT: 0 218 ILE cc_start: 0.8843 (pt) cc_final: 0.8580 (pt) REVERT: 0 236 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6834 (mt-10) REVERT: 0 270 ARG cc_start: 0.7334 (tpt-90) cc_final: 0.6789 (tpt90) REVERT: 0 365 GLN cc_start: 0.6578 (tt0) cc_final: 0.6110 (mt0) REVERT: 0 622 MET cc_start: 0.8855 (tpt) cc_final: 0.8477 (mmm) REVERT: 0 650 GLU cc_start: 0.7624 (mp0) cc_final: 0.7383 (mt-10) REVERT: 1 105 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6865 (mm-40) REVERT: 1 173 LYS cc_start: 0.6867 (mmtp) cc_final: 0.6402 (mmtt) REVERT: 1 178 LEU cc_start: 0.8437 (mt) cc_final: 0.8000 (tp) REVERT: 1 238 LYS cc_start: 0.7819 (pttm) cc_final: 0.7461 (tppt) REVERT: 1 299 GLU cc_start: 0.7354 (tt0) cc_final: 0.6629 (mt-10) REVERT: 1 318 ASP cc_start: 0.7230 (t0) cc_final: 0.6879 (t0) REVERT: 1 321 PHE cc_start: 0.7881 (m-10) cc_final: 0.7627 (m-80) REVERT: 1 346 ASP cc_start: 0.8059 (t0) cc_final: 0.7627 (t70) REVERT: 1 373 ASP cc_start: 0.7081 (t0) cc_final: 0.6731 (m-30) REVERT: 1 437 LEU cc_start: 0.8786 (tp) cc_final: 0.8427 (pp) REVERT: 1 560 PHE cc_start: 0.9027 (m-80) cc_final: 0.8697 (m-80) REVERT: 1 628 HIS cc_start: 0.8494 (t-90) cc_final: 0.7991 (t-90) REVERT: 2 13 TYR cc_start: 0.8474 (t80) cc_final: 0.8114 (t80) REVERT: 2 38 ILE cc_start: 0.8792 (tp) cc_final: 0.8523 (tp) REVERT: 2 48 MET cc_start: 0.8762 (tpp) cc_final: 0.8416 (tpt) REVERT: 2 88 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7652 (pt) REVERT: 2 97 MET cc_start: 0.6564 (mmm) cc_final: 0.5777 (mmm) REVERT: 2 428 GLU cc_start: 0.7007 (mp0) cc_final: 0.6662 (mp0) REVERT: 3 37 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7487 (mtp-110) REVERT: 3 56 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: 3 115 ASP cc_start: 0.6474 (t0) cc_final: 0.6117 (t0) REVERT: 4 81 GLN cc_start: 0.8854 (mm110) cc_final: 0.8566 (mm-40) REVERT: 4 229 ASP cc_start: 0.8033 (t0) cc_final: 0.7779 (t70) REVERT: 4 235 TYR cc_start: 0.9050 (t80) cc_final: 0.8723 (t80) REVERT: 4 281 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7811 (mtm-85) REVERT: 4 323 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8424 (tptp) REVERT: 5 59 SER cc_start: 0.7781 (m) cc_final: 0.7513 (p) REVERT: 6 134 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6893 (mm-30) REVERT: 6 215 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7004 (mt-10) REVERT: 6 252 ASP cc_start: 0.6971 (t0) cc_final: 0.6644 (t0) REVERT: 6 303 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7492 (tm-30) REVERT: 6 434 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7995 (mm-40) REVERT: 6 450 ASN cc_start: 0.8750 (p0) cc_final: 0.8459 (p0) REVERT: 7 124 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.6886 (ttm-80) REVERT: 7 220 TYR cc_start: 0.6292 (t80) cc_final: 0.5999 (t80) REVERT: 7 329 ARG cc_start: 0.7488 (mmm-85) cc_final: 0.7091 (mmm-85) REVERT: 7 349 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8220 (t0) REVERT: 7 381 SER cc_start: 0.8909 (m) cc_final: 0.8519 (p) REVERT: 7 404 LYS cc_start: 0.8343 (mmmm) cc_final: 0.7553 (mmtm) REVERT: 7 454 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8329 (m) REVERT: 7 571 ARG cc_start: 0.7537 (ptp90) cc_final: 0.7082 (tmm-80) REVERT: 7 576 LYS cc_start: 0.8197 (mttt) cc_final: 0.7795 (mtmm) REVERT: 7 615 LEU cc_start: 0.8580 (tp) cc_final: 0.8284 (tp) REVERT: 7 694 LYS cc_start: 0.7985 (tmtt) cc_final: 0.7708 (tppt) REVERT: A 15 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7422 (mttt) REVERT: A 112 LYS cc_start: 0.8024 (tttm) cc_final: 0.7414 (mtpp) REVERT: A 143 LYS cc_start: 0.7693 (ttmt) cc_final: 0.6794 (mptt) REVERT: A 169 ASN cc_start: 0.8740 (m-40) cc_final: 0.8172 (m110) REVERT: A 187 LYS cc_start: 0.7819 (pttt) cc_final: 0.7483 (pttm) REVERT: A 1454 MET cc_start: 0.5866 (mmm) cc_final: 0.4944 (mmt) REVERT: B 1178 ASN cc_start: 0.8051 (t0) cc_final: 0.7451 (t0) REVERT: D 180 LEU cc_start: 0.8133 (mt) cc_final: 0.7902 (mt) REVERT: F 103 MET cc_start: 0.7311 (mtp) cc_final: 0.6453 (mtt) REVERT: F 104 ASN cc_start: 0.8428 (t0) cc_final: 0.7786 (t0) REVERT: G 140 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7653 (ttmm) REVERT: W 135 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7325 (mm-30) REVERT: W 146 GLU cc_start: 0.7287 (mp0) cc_final: 0.7041 (mp0) REVERT: W 180 GLN cc_start: 0.7361 (tp40) cc_final: 0.6065 (tp40) REVERT: W 184 ASP cc_start: 0.7829 (m-30) cc_final: 0.7059 (m-30) REVERT: W 223 LYS cc_start: 0.8706 (tppt) cc_final: 0.8198 (tmtt) REVERT: W 285 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7238 (mmm160) REVERT: X 211 LYS cc_start: 0.7607 (mttp) cc_final: 0.7235 (mtmt) outliers start: 91 outliers final: 80 residues processed: 717 average time/residue: 0.2211 time to fit residues: 255.2918 Evaluate side-chains 732 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 646 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 96 GLU Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 235 ASP Chi-restraints excluded: chain 0 residue 304 GLU Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 440 LEU Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 675 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 355 ASP Chi-restraints excluded: chain 1 residue 427 SER Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 163 VAL Chi-restraints excluded: chain 2 residue 448 LEU Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 56 TYR Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 148 MET Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 7 residue 158 VAL Chi-restraints excluded: chain 7 residue 160 ILE Chi-restraints excluded: chain 7 residue 245 LEU Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 349 ASN Chi-restraints excluded: chain 7 residue 372 LYS Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 417 VAL Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 659 ASP Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 679 SER Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 740 HIS Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 285 ARG Chi-restraints excluded: chain X residue 235 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 23 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 85 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 340 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 92 ASN 1 258 ASN ** 1 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN 7 376 ASN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 GLN W 178 GLN ** X 199 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 = 0.3970 r_free = 0.3970 target = 0.187670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.124742 restraints weight = 39982.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.123991 restraints weight = 25704.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125082 restraints weight = 22196.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.126169 restraints weight = 19919.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.126371 restraints weight = 16789.059| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.469 34947 Z= 0.208 Angle : 0.689 59.007 47245 Z= 0.372 Chirality : 0.044 0.875 5378 Planarity : 0.004 0.055 5947 Dihedral : 8.208 105.238 4758 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 2.41 % Allowed : 17.33 % Favored : 80.26 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.78 (0.13), residues: 4122 helix: 1.54 (0.12), residues: 1936 sheet: -0.44 (0.23), residues: 519 loop : -0.29 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 4 146 TYR 0.085 0.002 TYR 1 583 PHE 0.027 0.001 PHE 7 316 TRP 0.020 0.001 TRP 1 29 HIS 0.009 0.001 HIS 6 449 Details of bonding type rmsd covalent geometry : bond 0.00530 (34902) covalent geometry : angle 0.67593 (47179) hydrogen bonds : bond 0.03627 ( 1587) hydrogen bonds : angle 4.24623 ( 4491) metal coordination : bond 0.00577 ( 44) metal coordination : angle 3.67012 ( 66) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8313.77 seconds wall clock time: 143 minutes 37.27 seconds (8617.27 seconds total)